From mgvallet.pro at gmail.com Mon Jan 4 16:55:56 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 4 Jan 2016 16:55:56 -0500 Subject: [Rtk-users] feldkamp application Message-ID: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Tue Jan 5 03:25:50 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 05 Jan 2016 09:25:50 +0100 Subject: [Rtk-users] feldkamp application In-Reply-To: References: Message-ID: <568B7E0E.9030904@uclouvain.be> Hi, and happy new year :) You can use the dataset provided for the motion-compensated reconstruction : http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Hope it helps, Cyril On 01/04/2016 10:55 PM, MG Vallet wrote: > Happy new year! > > Does someone have a data set, other than quadric phantoms, to test the > fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 5 05:16:50 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 5 Jan 2016 11:16:50 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: Message-ID: <568B9812.40404@creatis.insa-lyon.fr> Hi, I forgot to cc this email to the mailing list, in answers to mgv. Simon -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit To: MG Vallet Hi, There are vendor-specific examples available on the wiki: http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction You also have real patient data for 4D CBCT, e.g. http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Simon On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 5 16:50:09 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 5 Jan 2016 16:50:09 -0500 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: <568B9812.40404@creatis.insa-lyon.fr> References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: Thanks, Cyril and Simon. These applications seemed complicated to me, but it's only data reading that is. By the way, the command rtkfieldofview had no effect in the varian case (no error message, nor output file). Otherwise, everything's OK. 2016-01-05 5:16 GMT-05:00 Simon Rit : > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp > application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit > To: MG > Vallet > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet wrote: > >> Happy new year! >> >> Does someone have a data set, other than quadric phantoms, to test the >> fdk module ? >> It would be fine to add one to the wiki page >> http://wiki.openrtk.org/index.php/Main_Page#Applications >> >> mgv >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Mon Jan 11 09:34:58 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Mon, 11 Jan 2016 15:34:58 +0100 Subject: [Rtk-users] Parker weighting In-Reply-To: <56743FCB.3040102@creatis.insa-lyon.fr> References: <56667F38.6040604@creatis.insa-lyon.fr> <56743FCB.3040102@creatis.insa-lyon.fr> Message-ID: Dear Simon, I am sorry for the late reply. I also wish you a happy new year. I will recheck if there is any error during generating projection images. The projections are generated from a volume with our simulation tool. However, I generated projections from the volume with rtkforwardprojections and I re-reconstructed the volume with rtkfdk. I did not get any artifacts. I will contact you soon, if I have some results. Thank you very much for your help. Shiras On Fri, Dec 18, 2015 at 6:18 PM, Simon Rit wrote: > Hi Shiras, > Sorry for the delayed answer, times are busy. The way RTK computes the > spanned arc is from the second projection angle to the before last > projection angle, i.e., in your case > 209.609216488925-11.6067737022482 > so it's a span of 199 degrees and your cone angle is indeed too large. > Like I said, this part of RTK is perfectible and there is no way to change > this but change the code. > However, the source of artefacts might be something else. On simulated > data, I tried: > rtkprojectshepploganphantom --like original_proj.mhd -g > geometry_parker_corr.xml -o proj.mha > rtkfdk -p . -r proj.mha -o fdk.mha -g geometry_parker_corr.xml > and the result is not that bad. What do you think? Can you show us a > snapshot if sg's wrong in your opinion? > Simon > > > On 09/12/2015 11:01, Shiras Abdurahman wrote: > > Dear Simon, > > I am attaching the mhd files of projections. > > With regards, > Shiras > > On Tue, Dec 8, 2015 at 6:17 PM, Simon Rit > wrote: > >> Hi, >> The geometry files look ok to me. What is the projection information? If >> you're still getting the same message as before, I think it's because you >> don't have enough data. If you send the mhd file of the projections (just >> the mhd, not the raw data), I can try to test it on simulated data to let >> you know my feeling. >> Simon >> >> On Tue, Dec 8, 2015 at 5:41 PM, Shiras Abdurahman < >> shiraska at gmail.com> wrote: >> >>> Dear Simon, >>> >>> I tried this option and unfortunately it did not work. I added zero >>> projections and modified geometry files. However, I am getting same >>> artifacts in the volume. Voxel values changed a little bit that indicates >>> during backprojection it still considers extreme projections. I am also >>> getting an output message same as before. >>> >>> I am attaching geometry files. >>> >>> With regards, >>> Shiras >>> >>> On Tue, Dec 8, 2015 at 10:15 AM, Simon Rit < >>> simon.rit at creatis.insa-lyon.fr> wrote: >>> >>>> So calling AddProjection before and after the loop with an adequate >>>> gantry_angle should work. >>>> Simon >>>> >>>> On Tue, Dec 8, 2015 at 9:52 AM, Shiras Abdurahman < >>>> shiraska at gmail.com> wrote: >>>> >>>>> Drear Simon, >>>>> >>>>> I generate the geometry with system geometry parameters and using >>>>> AddProjection method. >>>>> >>>>> Here is the code >>>>> >>>>> >>>>> rtk::ThreeDCircularProjectionGeometry::Pointer rtk_sys_geometry_; >>>>> rtk_sys_geometry_ = rtk::ThreeDCircularProjectionGeometry::New(); >>>>> for (uint16_t proj_index = 0; proj_index < num_projections_; >>>>> proj_index++) >>>>> { >>>>> >>>>> rtk_sys_geometry_->AddProjection(rtk_geom_params_.at(proj_index).sid_mm, >>>>> rtk_geom_params_.at(proj_index).sdd_mm, >>>>> rtk_geom_params_.at(proj_index).gantry_angle_deg, >>>>> rtk_geom_params_.at(proj_index).proj_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).proj_offset_y_mm, >>>>> rtk_geom_params_.at(proj_index).out_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).in_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).src_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).src_offset_y_mm); >>>>> } >>>>> >>>>> And then write to xml file. >>>>> >>>>> Shiras >>>>> >>>>> >>>>> >>>>> On Tue, Dec 8, 2015 at 9:23 AM, Simon Rit < >>>>> simon.rit at creatis.insa-lyon.fr> wrote: >>>>> >>>>>> Hi, >>>>>> rtkfdk.cxx just read the geometry from a file so the best is to >>>>>> modify the geometry file. How do you generate the geometry? >>>>>> For example, if you use rtksimulated geometry, let's say that you >>>>>> were using: >>>>>> rtksimulatedgeometry -n 200 -a 200 -o g.xml >>>>>> then you'll have to replace it with >>>>>> rtksimulatedgeometry -n 202 -a 202 -o g.xml -f -1 >>>>>> Don't forget to add dummy projection at the beginning and the end. If >>>>>> you use a more complex geometry, maybe SimpleRTK >>>>>> can be helpful >>>>>> (I'd use that) or you'd have to modify the cxx code to add these additional >>>>>> projections in the geometry and the projection stack. >>>>>> Simon >>>>>> >>>>>> >>>>>> On Tue, Dec 8, 2015 at 8:51 AM, Shiras Abdurahman < >>>>>> shiraska at gmail.com> wrote: >>>>>> >>>>>>> Dear Simon, >>>>>>> >>>>>>> Thanks a lot for the reply. Can you please inform me how can I set >>>>>>> where the arc starts? >>>>>>> Do I need to modify geometry also? >>>>>>> If you can point the line of code rtkfdk.cxx, it will be really >>>>>>> helpful. >>>>>>> >>>>>>> With regards, >>>>>>> Shiras >>>>>>> >>>>>>> On Tue, Dec 8, 2015 at 7:56 AM, Simon Rit < >>>>>>> simon.rit at creatis.insa-lyon.fr> >>>>>>> wrote: >>>>>>> >>>>>>>> Dear Shiras, >>>>>>>> Yes, for practical reasons the first and the last projections are >>>>>>>> set to 0 and the arc used in the Parker weighting starts between the first >>>>>>>> two projections and ends between the lasts two projections. There is a >>>>>>>> simple solution: add a projection at the beginning and the end of the arc, >>>>>>>> which can contain any pixel values but should be set where you want this >>>>>>>> arc to start. In the future, I think someone should once take the time to >>>>>>>> correct this but I haven't so far. I'll keep you posted on the mailing list >>>>>>>> when it's corrected. >>>>>>>> Simon >>>>>>>> >>>>>>>> On 07/12/2015 12:04, Shiras Abdurahman wrote: >>>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I am trying to reconstruct a volume from projection data generated >>>>>>>> with C-arm CT. There are 248 projections with an angular range of 199 >>>>>>>> degree. Technically, parker weighting should run without any problems. >>>>>>>> However, I am getting an output message that "You do not have enough data >>>>>>>> for proper parker weighting". After parker weighting, the two extreme >>>>>>>> projections (projection number 1 and 248) were completely zero and thus >>>>>>>> reconstructed volume contained artifacts. When I increased the angular >>>>>>>> range, this problem did not happen. How can I solve this problem without >>>>>>>> increasing angular range? Is there any threshold constant that I can change >>>>>>>> in command line or in my code? >>>>>>>> >>>>>>>> I really appreciate any help you can provide. >>>>>>>> >>>>>>>> With regards, >>>>>>>> Shiras >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 12 07:47:46 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 12 Jan 2016 13:47:46 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: <5694F5F2.4060702@creatis.insa-lyon.fr> Hi, There was a typo on the folder path (../Scan0 instead of Scan0). Was that the problem? I checked and it has the expected effect, i.e., setting to 0 everything outside the FOV. Simon On 05/01/2016 22:50, MG Vallet wrote: > Thanks, Cyril and Simon. > These applications seemed complicated to me, but it's only data > reading that is. > By the way, the command rtkfieldofview had no effect in the varian > case (no error message, nor output file). Otherwise, everything's OK. > > 2016-01-05 5:16 GMT-05:00 Simon Rit >: > > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- > Subject: Re: [Rtk-users] feldkamp application > Date: Tue, 5 Jan 2016 08:40:00 +0100 > From: Simon Rit > > To: MG Vallet > > > > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: > > Happy new year! > > Does someone have a data set, other than quadric phantoms, to > test the fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Wed Jan 13 07:42:45 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Wed, 13 Jan 2016 13:42:45 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry Message-ID: Dear all, I am trying to generate geometry xml file with rtkReg23ProjectionGeometry after decomposing projection matrix. One of the argument to the function AddReg23Projection is detector position. I assume that, it is the position vector of the center of the first pixel in world co-ordinates. This will be used for computing the projection offset parameters by projecting detector origin vector onto the u and v axis of the detector. If that is the case, do we need to change the offset parameters of each projection in the mhd file. Will this create problems during displaced detector correction? With regards, Shiras -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 13 13:31:23 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Jan 2016 19:31:23 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry In-Reply-To: References: Message-ID: <569697FB.1020804@creatis.insa-lyon.fr> Hi, Wrong assumption. It's the coordinate of point (0,0) in the coordinate of the projection image in the word coordinates, it's not the coordinate of the center of the first pixel. This is mentioned in the geometry description file on the wiki. You should not change the mhd parameters. If you want to account for offset parameters that change from projection to projection, you can put that offset in the computation of the detector position in world coordinates. Simon On 13/01/2016 13:42, Shiras Abdurahman wrote: > Dear all, > > I am trying to generate geometry xml file with > rtkReg23ProjectionGeometry after decomposing projection matrix. One of > the argument to the function AddReg23Projection is detector position. > I assume that, it is the position vector of the center of the first > pixel in world co-ordinates. This will be used for computing the > projection offset parameters by projecting detector origin vector onto > the u and v axis of the detector. If that is the case, do we need to > change the offset parameters of each projection in the mhd file. Will > this create problems during displaced detector correction? > > > With regards, > Shiras > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 10:19:12 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 10:19:12 -0500 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from https://zenodo.org/record/16539. This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts. I am not 100% sure I properly set the geometry parameters. Regards, mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sophiaBeadsCentralSlide.jpg Type: image/jpeg Size: 55394 bytes Desc: not available URL: From cyril.mory at uclouvain.be Tue Jan 19 10:33:02 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 19 Jan 2016 16:33:02 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: <569E572E.20203@uclouvain.be> Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit : > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% > sure I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users --- L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 14:02:45 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 14:02:45 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <569E572E.20203@uclouvain.be> References: <569E572E.20203@uclouvain.be> Message-ID: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > > ------------------------------ > [image: Avast logo] > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 20 03:33:47 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 20 Jan 2016 09:33:47 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > >> Hi, >> >> It looks like the geometry is wrong indeed, because I have never seen >> such artifacts. >> >> Hope that helps, >> Cyril >> >> >> Le 19/01/2016 16:19, MG Vallet a ?crit : >> >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data set from >> https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has been scanned. >> >> Attached is a view of the reconstructed central slice. It is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the proper term) >> >> My question is if these are simply expected artifacts. I am not 100% >> sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> >> ------------------------------ >> [image: Avast logo] >> >> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >> logiciel antivirus Avast. >> www.avast.com >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkfdk.sh Type: application/x-sh Size: 404 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: snapshot.jpg Type: image/jpeg Size: 95222 bytes Desc: not available URL: From mgvallet.pro at gmail.com Thu Jan 21 14:02:28 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 21 Jan 2016 14:02:28 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was SophiaBeads_512_averaged. Regarding the pre-processing mentioned by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > >> Thanks Cyril! >> going to carefully check my inputs and I give you some news. >> mgv >> >> 2016-01-19 10:33 GMT-05:00 Cyril Mory : >> >>> Hi, >>> >>> It looks like the geometry is wrong indeed, because I have never seen >>> such artifacts. >>> >>> Hope that helps, >>> Cyril >>> >>> >>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>> >>> Dear rtk-users, >>> >>> I applied the FDKConeBeamReconstructionFilter to a data set from >>> https://zenodo.org/record/16539. >>> This is a plastic tube filled with glass beads that has been scanned. >>> >>> Attached is a view of the reconstructed central slice. It is found that: >>> >>> 1. the beads are quickly deformed outside the center >>> 2. each one has a halo, or a shadow (dont know the proper term) >>> >>> My question is if these are simply expected artifacts. I am not 100% >>> sure I properly set the geometry parameters. >>> >>> Regards, >>> mgv >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >>> >>> ------------------------------ >>> [image: Avast logo] >>> >>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>> logiciel antivirus Avast. >>> www.avast.com >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_offset.jpg Type: image/jpeg Size: 52844 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Thu Jan 21 14:22:55 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Jan 2016 20:22:55 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: <56A1300F.1090509@creatis.insa-lyon.fr> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center > must effectively be offset (4.8 mm in both directions). For the > attached image, I also increases sdd and sid by a factor 1000, just in > case I would be wrong in units. It reduces the first default I pointed > out in my first message. Also note that my input dataset was > SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is > it as simple as the FDK filter assumes that the input is intensity, > but the dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit >: > > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems > that what is provided is directly the line integral. RTK will > process the tif images as if it were a photon count so I converted > the tif projections to mha to avoid this. For the conversion, I > used another piece of software but you can easily do the same > thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better > result. I have however a geometry problem. I think they provide a > Matlab piece of code to get the center of rotation. If you can run > it and find out what is this center, then you can use it to > configure the geometry better with the options --proj_iso_x and > --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet > wrote: > > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory >: > > Hi, > > It looks like the geometry is wrong indeed, because I have > never seen such artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data >> set from https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has >> been scanned. >> >> Attached is a view of the reconstructed central slice. It >> is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the >> proper term) >> >> My question is if these are simply expected artifacts. I >> am not 100% sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> >> http://public.kitware.com/mailman/listinfo/rtk-users > > > > ------------------------------------------------------------------------ > Avast logo > > L'absence de virus dans ce courrier ?lectronique a ?t? > v?rifi?e par le logiciel antivirus Avast. > www.avast.com > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 25 11:48:35 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 25 Jan 2016 11:48:35 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <56A1300F.1090509@creatis.insa-lyon.fr> References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > >> Hi, >> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >> is provided is directly the line integral. RTK will process the tif images >> as if it were a photon count so I converted the tif projections to mha to >> avoid this. For the conversion, I used another piece of software but you >> can easily do the same thing with SimpleRTK. >> Second, I used the enclosed script which gives me a much better result. I >> have however a geometry problem. I think they provide a Matlab piece of >> code to get the center of rotation. If you can run it and find out what is >> this center, then you can use it to configure the geometry better with the >> options --proj_iso_x and --proj_iso_y. >> Good luck, >> Simon >> >> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >> mgvallet.pro at gmail.com> wrote: >> >>> Thanks Cyril! >>> going to carefully check my inputs and I give you some news. >>> mgv >>> >>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>> cyril.mory at uclouvain.be>: >>> >>>> Hi, >>>> >>>> It looks like the geometry is wrong indeed, because I have never seen >>>> such artifacts. >>>> >>>> Hope that helps, >>>> Cyril >>>> >>>> >>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>> >>>> Dear rtk-users, >>>> >>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>> https://zenodo.org/record/16539. >>>> This is a plastic tube filled with glass beads that has been scanned. >>>> >>>> Attached is a view of the reconstructed central slice. It is found that: >>>> >>>> 1. the beads are quickly deformed outside the center >>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>> >>>> My question is if these are simply expected artifacts. I am not 100% >>>> sure I properly set the geometry parameters. >>>> >>>> Regards, >>>> mgv >>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> [image: Avast logo] >>>> >>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>> logiciel antivirus Avast. >>>> www.avast.com >>>> >>>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_log.jpg Type: image/jpeg Size: 17331 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 26 07:23:58 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Jan 2016 13:23:58 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > Hi Simon, > > this was a point I missed. I had to do the log mapping. > > I must say, I do not use RTK from shell. I just plugged the objects > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > MG > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > >> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the >> line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the >> projections and converts them depending on the type: for mha or mhd, it >> just reads it and nothing else. For tif, it assumes that I is passed, try >> to guess I0 (or gets it from the cmd line) and computes ln(I0/I). >> So from each tif projection, instead of letting them go through the >> ProjectionsReader in RTK, directly use the ImageReader, stack them and pass >> it to the reconstruction algorithm. In other words, if you use SimpleRTK, >> use ImageSeriesReader instead of ProjectionsReader. >> Regarding the geometry, it would be nice to be confident in the geometry >> parameters, maybe from their Matlab code? >> Simon >> >> >> On 21/01/2016 20:02, MG Vallet wrote: >> >> Hi Simon and Cyril, >> >> I really appreciate your insight. >> >> By examining the parameters of the acquisition, I saw that the center >> must effectively be offset (4.8 mm in both directions). For the attached >> image, I also increases sdd and sid by a factor 1000, just in case I would >> be wrong in units. It reduces the first default I pointed out in my first >> message. Also note that my input dataset was SophiaBeads_512_averaged. >> >> Regarding the pre-processing mentioned by Simon, I need more help. Is it >> as simple as the FDK filter assumes that the input is intensity, but the >> dataset provides -ln(I/I0) ? >> >> Regards, >> mg >> >> 2016-01-20 3:33 GMT-05:00 Simon Rit : >> >>> Hi, >>> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >>> is provided is directly the line integral. RTK will process the tif images >>> as if it were a photon count so I converted the tif projections to mha to >>> avoid this. For the conversion, I used another piece of software but you >>> can easily do the same thing with SimpleRTK. >>> Second, I used the enclosed script which gives me a much better result. >>> I have however a geometry problem. I think they provide a Matlab piece of >>> code to get the center of rotation. If you can run it and find out what is >>> this center, then you can use it to configure the geometry better with the >>> options --proj_iso_x and --proj_iso_y. >>> Good luck, >>> Simon >>> >>> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >>> mgvallet.pro at gmail.com> wrote: >>> >>>> Thanks Cyril! >>>> going to carefully check my inputs and I give you some news. >>>> mgv >>>> >>>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>>> cyril.mory at uclouvain.be>: >>>> >>>>> Hi, >>>>> >>>>> It looks like the geometry is wrong indeed, because I have never seen >>>>> such artifacts. >>>>> >>>>> Hope that helps, >>>>> Cyril >>>>> >>>>> >>>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>>> >>>>> Dear rtk-users, >>>>> >>>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>>> https://zenodo.org/record/16539. >>>>> This is a plastic tube filled with glass beads that has been scanned. >>>>> >>>>> Attached is a view of the reconstructed central slice. It is found >>>>> that: >>>>> >>>>> 1. the beads are quickly deformed outside the center >>>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>>> >>>>> My question is if these are simply expected artifacts. I am not 100% >>>>> sure I properly set the geometry parameters. >>>>> >>>>> Regards, >>>>> mgv >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> [image: Avast logo] >>>>> >>>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>>> logiciel antivirus Avast. >>>>> www.avast.com >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Jan 26 17:17:01 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 26 Jan 2016 23:17:01 +0100 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Hi MG, Sometimes, the progressive deformation from the center of rotation to the edge of the image is caused by wrong sdd/sid ratio. Such as change in the geometry will lead to distortion of the image and wrong magnification. Maybe you can play with that parameter and report your result. Cheers, Louie Sent from Mail for Windows 10 From: Simon Rit Sent: Tuesday, January 26, 2016 13:24 To: MG Vallet Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Sophia beads reconstruction Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and?ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was?SophiaBeads_512_averaged. Regarding the pre-processing?mentioned?by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit?: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from?https://zenodo.org/record/16539.? This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts.?I am not 100% sure I properly set the geometry parameters. Regards, mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. www.avast.com _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Thu Jan 28 16:27:15 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 28 Jan 2016 16:27:15 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: Louie, I played with sdd and sid, following your advise. But they have few effect, clearly less effect than proj_iso_x. And none of these parameters can significantly improve my result. Simon, I carefully checked every input data and I cant see what I did wrong. I want first to reproduce your output. You said earlier it's easy to convert a series of tiff image into a mha file using SimpleRTK. Do you mean by writing a short program, or is it possible from the command line ? MG 2016-01-26 17:17 GMT-05:00 louie L : > Hi MG, > > > > Sometimes, the progressive deformation from the center of rotation to the > edge of the image is caused by wrong sdd/sid ratio. Such as change in the > geometry will lead to distortion of the image and wrong magnification. > > Maybe you can play with that parameter and report your result. > > > > Cheers, > > Louie > > > > Sent from Mail for > Windows 10 > > > > > *From: *Simon Rit > *Sent: *Tuesday, January 26, 2016 13:24 > *To: *MG Vallet > *Cc: *rtk-users at public.kitware.com > *Subject: *Re: [Rtk-users] Sophia beads reconstruction > > > > Hi, > > I think it's likely a problem with parameters. The best would be to obtain > them from the Matlab code they provide. > > Good luck, > > Simon > > > > On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > > Hi Simon, > > > > this was a point I missed. I had to do the log mapping. > > > > I must say, I do not use RTK from shell. I just plugged the objects > > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > > > MG > > > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > > > I really appreciate your insight. > > > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > > > Regards, > > mg > > > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > > Hi, > > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > > Good luck, > > Simon > > > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > > Thanks Cyril! > > going to carefully check my inputs and I give you some news. > > mgv > > > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > > This is a plastic tube filled with glass beads that has been scanned. > > > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > > > Regards, > > mgv > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 4 16:55:56 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 4 Jan 2016 16:55:56 -0500 Subject: [Rtk-users] feldkamp application Message-ID: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Tue Jan 5 03:25:50 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 05 Jan 2016 09:25:50 +0100 Subject: [Rtk-users] feldkamp application In-Reply-To: References: Message-ID: <568B7E0E.9030904@uclouvain.be> Hi, and happy new year :) You can use the dataset provided for the motion-compensated reconstruction : http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Hope it helps, Cyril On 01/04/2016 10:55 PM, MG Vallet wrote: > Happy new year! > > Does someone have a data set, other than quadric phantoms, to test the > fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 5 05:16:50 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 5 Jan 2016 11:16:50 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: Message-ID: <568B9812.40404@creatis.insa-lyon.fr> Hi, I forgot to cc this email to the mailing list, in answers to mgv. Simon -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit To: MG Vallet Hi, There are vendor-specific examples available on the wiki: http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction You also have real patient data for 4D CBCT, e.g. http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Simon On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 5 16:50:09 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 5 Jan 2016 16:50:09 -0500 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: <568B9812.40404@creatis.insa-lyon.fr> References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: Thanks, Cyril and Simon. These applications seemed complicated to me, but it's only data reading that is. By the way, the command rtkfieldofview had no effect in the varian case (no error message, nor output file). Otherwise, everything's OK. 2016-01-05 5:16 GMT-05:00 Simon Rit : > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp > application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit > To: MG > Vallet > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet wrote: > >> Happy new year! >> >> Does someone have a data set, other than quadric phantoms, to test the >> fdk module ? >> It would be fine to add one to the wiki page >> http://wiki.openrtk.org/index.php/Main_Page#Applications >> >> mgv >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Mon Jan 11 09:34:58 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Mon, 11 Jan 2016 15:34:58 +0100 Subject: [Rtk-users] Parker weighting In-Reply-To: <56743FCB.3040102@creatis.insa-lyon.fr> References: <56667F38.6040604@creatis.insa-lyon.fr> <56743FCB.3040102@creatis.insa-lyon.fr> Message-ID: Dear Simon, I am sorry for the late reply. I also wish you a happy new year. I will recheck if there is any error during generating projection images. The projections are generated from a volume with our simulation tool. However, I generated projections from the volume with rtkforwardprojections and I re-reconstructed the volume with rtkfdk. I did not get any artifacts. I will contact you soon, if I have some results. Thank you very much for your help. Shiras On Fri, Dec 18, 2015 at 6:18 PM, Simon Rit wrote: > Hi Shiras, > Sorry for the delayed answer, times are busy. The way RTK computes the > spanned arc is from the second projection angle to the before last > projection angle, i.e., in your case > 209.609216488925-11.6067737022482 > so it's a span of 199 degrees and your cone angle is indeed too large. > Like I said, this part of RTK is perfectible and there is no way to change > this but change the code. > However, the source of artefacts might be something else. On simulated > data, I tried: > rtkprojectshepploganphantom --like original_proj.mhd -g > geometry_parker_corr.xml -o proj.mha > rtkfdk -p . -r proj.mha -o fdk.mha -g geometry_parker_corr.xml > and the result is not that bad. What do you think? Can you show us a > snapshot if sg's wrong in your opinion? > Simon > > > On 09/12/2015 11:01, Shiras Abdurahman wrote: > > Dear Simon, > > I am attaching the mhd files of projections. > > With regards, > Shiras > > On Tue, Dec 8, 2015 at 6:17 PM, Simon Rit > wrote: > >> Hi, >> The geometry files look ok to me. What is the projection information? If >> you're still getting the same message as before, I think it's because you >> don't have enough data. If you send the mhd file of the projections (just >> the mhd, not the raw data), I can try to test it on simulated data to let >> you know my feeling. >> Simon >> >> On Tue, Dec 8, 2015 at 5:41 PM, Shiras Abdurahman < >> shiraska at gmail.com> wrote: >> >>> Dear Simon, >>> >>> I tried this option and unfortunately it did not work. I added zero >>> projections and modified geometry files. However, I am getting same >>> artifacts in the volume. Voxel values changed a little bit that indicates >>> during backprojection it still considers extreme projections. I am also >>> getting an output message same as before. >>> >>> I am attaching geometry files. >>> >>> With regards, >>> Shiras >>> >>> On Tue, Dec 8, 2015 at 10:15 AM, Simon Rit < >>> simon.rit at creatis.insa-lyon.fr> wrote: >>> >>>> So calling AddProjection before and after the loop with an adequate >>>> gantry_angle should work. >>>> Simon >>>> >>>> On Tue, Dec 8, 2015 at 9:52 AM, Shiras Abdurahman < >>>> shiraska at gmail.com> wrote: >>>> >>>>> Drear Simon, >>>>> >>>>> I generate the geometry with system geometry parameters and using >>>>> AddProjection method. >>>>> >>>>> Here is the code >>>>> >>>>> >>>>> rtk::ThreeDCircularProjectionGeometry::Pointer rtk_sys_geometry_; >>>>> rtk_sys_geometry_ = rtk::ThreeDCircularProjectionGeometry::New(); >>>>> for (uint16_t proj_index = 0; proj_index < num_projections_; >>>>> proj_index++) >>>>> { >>>>> >>>>> rtk_sys_geometry_->AddProjection(rtk_geom_params_.at(proj_index).sid_mm, >>>>> rtk_geom_params_.at(proj_index).sdd_mm, >>>>> rtk_geom_params_.at(proj_index).gantry_angle_deg, >>>>> rtk_geom_params_.at(proj_index).proj_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).proj_offset_y_mm, >>>>> rtk_geom_params_.at(proj_index).out_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).in_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).src_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).src_offset_y_mm); >>>>> } >>>>> >>>>> And then write to xml file. >>>>> >>>>> Shiras >>>>> >>>>> >>>>> >>>>> On Tue, Dec 8, 2015 at 9:23 AM, Simon Rit < >>>>> simon.rit at creatis.insa-lyon.fr> wrote: >>>>> >>>>>> Hi, >>>>>> rtkfdk.cxx just read the geometry from a file so the best is to >>>>>> modify the geometry file. How do you generate the geometry? >>>>>> For example, if you use rtksimulated geometry, let's say that you >>>>>> were using: >>>>>> rtksimulatedgeometry -n 200 -a 200 -o g.xml >>>>>> then you'll have to replace it with >>>>>> rtksimulatedgeometry -n 202 -a 202 -o g.xml -f -1 >>>>>> Don't forget to add dummy projection at the beginning and the end. If >>>>>> you use a more complex geometry, maybe SimpleRTK >>>>>> can be helpful >>>>>> (I'd use that) or you'd have to modify the cxx code to add these additional >>>>>> projections in the geometry and the projection stack. >>>>>> Simon >>>>>> >>>>>> >>>>>> On Tue, Dec 8, 2015 at 8:51 AM, Shiras Abdurahman < >>>>>> shiraska at gmail.com> wrote: >>>>>> >>>>>>> Dear Simon, >>>>>>> >>>>>>> Thanks a lot for the reply. Can you please inform me how can I set >>>>>>> where the arc starts? >>>>>>> Do I need to modify geometry also? >>>>>>> If you can point the line of code rtkfdk.cxx, it will be really >>>>>>> helpful. >>>>>>> >>>>>>> With regards, >>>>>>> Shiras >>>>>>> >>>>>>> On Tue, Dec 8, 2015 at 7:56 AM, Simon Rit < >>>>>>> simon.rit at creatis.insa-lyon.fr> >>>>>>> wrote: >>>>>>> >>>>>>>> Dear Shiras, >>>>>>>> Yes, for practical reasons the first and the last projections are >>>>>>>> set to 0 and the arc used in the Parker weighting starts between the first >>>>>>>> two projections and ends between the lasts two projections. There is a >>>>>>>> simple solution: add a projection at the beginning and the end of the arc, >>>>>>>> which can contain any pixel values but should be set where you want this >>>>>>>> arc to start. In the future, I think someone should once take the time to >>>>>>>> correct this but I haven't so far. I'll keep you posted on the mailing list >>>>>>>> when it's corrected. >>>>>>>> Simon >>>>>>>> >>>>>>>> On 07/12/2015 12:04, Shiras Abdurahman wrote: >>>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I am trying to reconstruct a volume from projection data generated >>>>>>>> with C-arm CT. There are 248 projections with an angular range of 199 >>>>>>>> degree. Technically, parker weighting should run without any problems. >>>>>>>> However, I am getting an output message that "You do not have enough data >>>>>>>> for proper parker weighting". After parker weighting, the two extreme >>>>>>>> projections (projection number 1 and 248) were completely zero and thus >>>>>>>> reconstructed volume contained artifacts. When I increased the angular >>>>>>>> range, this problem did not happen. How can I solve this problem without >>>>>>>> increasing angular range? Is there any threshold constant that I can change >>>>>>>> in command line or in my code? >>>>>>>> >>>>>>>> I really appreciate any help you can provide. >>>>>>>> >>>>>>>> With regards, >>>>>>>> Shiras >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 12 07:47:46 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 12 Jan 2016 13:47:46 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: <5694F5F2.4060702@creatis.insa-lyon.fr> Hi, There was a typo on the folder path (../Scan0 instead of Scan0). Was that the problem? I checked and it has the expected effect, i.e., setting to 0 everything outside the FOV. Simon On 05/01/2016 22:50, MG Vallet wrote: > Thanks, Cyril and Simon. > These applications seemed complicated to me, but it's only data > reading that is. > By the way, the command rtkfieldofview had no effect in the varian > case (no error message, nor output file). Otherwise, everything's OK. > > 2016-01-05 5:16 GMT-05:00 Simon Rit >: > > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- > Subject: Re: [Rtk-users] feldkamp application > Date: Tue, 5 Jan 2016 08:40:00 +0100 > From: Simon Rit > > To: MG Vallet > > > > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: > > Happy new year! > > Does someone have a data set, other than quadric phantoms, to > test the fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Wed Jan 13 07:42:45 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Wed, 13 Jan 2016 13:42:45 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry Message-ID: Dear all, I am trying to generate geometry xml file with rtkReg23ProjectionGeometry after decomposing projection matrix. One of the argument to the function AddReg23Projection is detector position. I assume that, it is the position vector of the center of the first pixel in world co-ordinates. This will be used for computing the projection offset parameters by projecting detector origin vector onto the u and v axis of the detector. If that is the case, do we need to change the offset parameters of each projection in the mhd file. Will this create problems during displaced detector correction? With regards, Shiras -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 13 13:31:23 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Jan 2016 19:31:23 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry In-Reply-To: References: Message-ID: <569697FB.1020804@creatis.insa-lyon.fr> Hi, Wrong assumption. It's the coordinate of point (0,0) in the coordinate of the projection image in the word coordinates, it's not the coordinate of the center of the first pixel. This is mentioned in the geometry description file on the wiki. You should not change the mhd parameters. If you want to account for offset parameters that change from projection to projection, you can put that offset in the computation of the detector position in world coordinates. Simon On 13/01/2016 13:42, Shiras Abdurahman wrote: > Dear all, > > I am trying to generate geometry xml file with > rtkReg23ProjectionGeometry after decomposing projection matrix. One of > the argument to the function AddReg23Projection is detector position. > I assume that, it is the position vector of the center of the first > pixel in world co-ordinates. This will be used for computing the > projection offset parameters by projecting detector origin vector onto > the u and v axis of the detector. If that is the case, do we need to > change the offset parameters of each projection in the mhd file. Will > this create problems during displaced detector correction? > > > With regards, > Shiras > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 10:19:12 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 10:19:12 -0500 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from https://zenodo.org/record/16539. This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts. I am not 100% sure I properly set the geometry parameters. Regards, mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sophiaBeadsCentralSlide.jpg Type: image/jpeg Size: 55394 bytes Desc: not available URL: From cyril.mory at uclouvain.be Tue Jan 19 10:33:02 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 19 Jan 2016 16:33:02 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: <569E572E.20203@uclouvain.be> Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit : > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% > sure I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users --- L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 14:02:45 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 14:02:45 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <569E572E.20203@uclouvain.be> References: <569E572E.20203@uclouvain.be> Message-ID: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > > ------------------------------ > [image: Avast logo] > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 20 03:33:47 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 20 Jan 2016 09:33:47 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > >> Hi, >> >> It looks like the geometry is wrong indeed, because I have never seen >> such artifacts. >> >> Hope that helps, >> Cyril >> >> >> Le 19/01/2016 16:19, MG Vallet a ?crit : >> >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data set from >> https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has been scanned. >> >> Attached is a view of the reconstructed central slice. It is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the proper term) >> >> My question is if these are simply expected artifacts. I am not 100% >> sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> >> ------------------------------ >> [image: Avast logo] >> >> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >> logiciel antivirus Avast. >> www.avast.com >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkfdk.sh Type: application/x-sh Size: 404 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: snapshot.jpg Type: image/jpeg Size: 95222 bytes Desc: not available URL: From mgvallet.pro at gmail.com Thu Jan 21 14:02:28 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 21 Jan 2016 14:02:28 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was SophiaBeads_512_averaged. Regarding the pre-processing mentioned by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > >> Thanks Cyril! >> going to carefully check my inputs and I give you some news. >> mgv >> >> 2016-01-19 10:33 GMT-05:00 Cyril Mory : >> >>> Hi, >>> >>> It looks like the geometry is wrong indeed, because I have never seen >>> such artifacts. >>> >>> Hope that helps, >>> Cyril >>> >>> >>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>> >>> Dear rtk-users, >>> >>> I applied the FDKConeBeamReconstructionFilter to a data set from >>> https://zenodo.org/record/16539. >>> This is a plastic tube filled with glass beads that has been scanned. >>> >>> Attached is a view of the reconstructed central slice. It is found that: >>> >>> 1. the beads are quickly deformed outside the center >>> 2. each one has a halo, or a shadow (dont know the proper term) >>> >>> My question is if these are simply expected artifacts. I am not 100% >>> sure I properly set the geometry parameters. >>> >>> Regards, >>> mgv >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >>> >>> ------------------------------ >>> [image: Avast logo] >>> >>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>> logiciel antivirus Avast. >>> www.avast.com >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_offset.jpg Type: image/jpeg Size: 52844 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Thu Jan 21 14:22:55 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Jan 2016 20:22:55 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: <56A1300F.1090509@creatis.insa-lyon.fr> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center > must effectively be offset (4.8 mm in both directions). For the > attached image, I also increases sdd and sid by a factor 1000, just in > case I would be wrong in units. It reduces the first default I pointed > out in my first message. Also note that my input dataset was > SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is > it as simple as the FDK filter assumes that the input is intensity, > but the dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit >: > > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems > that what is provided is directly the line integral. RTK will > process the tif images as if it were a photon count so I converted > the tif projections to mha to avoid this. For the conversion, I > used another piece of software but you can easily do the same > thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better > result. I have however a geometry problem. I think they provide a > Matlab piece of code to get the center of rotation. If you can run > it and find out what is this center, then you can use it to > configure the geometry better with the options --proj_iso_x and > --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet > wrote: > > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory >: > > Hi, > > It looks like the geometry is wrong indeed, because I have > never seen such artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data >> set from https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has >> been scanned. >> >> Attached is a view of the reconstructed central slice. It >> is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the >> proper term) >> >> My question is if these are simply expected artifacts. I >> am not 100% sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> >> http://public.kitware.com/mailman/listinfo/rtk-users > > > > ------------------------------------------------------------------------ > Avast logo > > L'absence de virus dans ce courrier ?lectronique a ?t? > v?rifi?e par le logiciel antivirus Avast. > www.avast.com > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 25 11:48:35 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 25 Jan 2016 11:48:35 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <56A1300F.1090509@creatis.insa-lyon.fr> References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > >> Hi, >> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >> is provided is directly the line integral. RTK will process the tif images >> as if it were a photon count so I converted the tif projections to mha to >> avoid this. For the conversion, I used another piece of software but you >> can easily do the same thing with SimpleRTK. >> Second, I used the enclosed script which gives me a much better result. I >> have however a geometry problem. I think they provide a Matlab piece of >> code to get the center of rotation. If you can run it and find out what is >> this center, then you can use it to configure the geometry better with the >> options --proj_iso_x and --proj_iso_y. >> Good luck, >> Simon >> >> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >> mgvallet.pro at gmail.com> wrote: >> >>> Thanks Cyril! >>> going to carefully check my inputs and I give you some news. >>> mgv >>> >>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>> cyril.mory at uclouvain.be>: >>> >>>> Hi, >>>> >>>> It looks like the geometry is wrong indeed, because I have never seen >>>> such artifacts. >>>> >>>> Hope that helps, >>>> Cyril >>>> >>>> >>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>> >>>> Dear rtk-users, >>>> >>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>> https://zenodo.org/record/16539. >>>> This is a plastic tube filled with glass beads that has been scanned. >>>> >>>> Attached is a view of the reconstructed central slice. It is found that: >>>> >>>> 1. the beads are quickly deformed outside the center >>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>> >>>> My question is if these are simply expected artifacts. I am not 100% >>>> sure I properly set the geometry parameters. >>>> >>>> Regards, >>>> mgv >>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> [image: Avast logo] >>>> >>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>> logiciel antivirus Avast. >>>> www.avast.com >>>> >>>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_log.jpg Type: image/jpeg Size: 17331 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 26 07:23:58 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Jan 2016 13:23:58 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > Hi Simon, > > this was a point I missed. I had to do the log mapping. > > I must say, I do not use RTK from shell. I just plugged the objects > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > MG > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > >> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the >> line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the >> projections and converts them depending on the type: for mha or mhd, it >> just reads it and nothing else. For tif, it assumes that I is passed, try >> to guess I0 (or gets it from the cmd line) and computes ln(I0/I). >> So from each tif projection, instead of letting them go through the >> ProjectionsReader in RTK, directly use the ImageReader, stack them and pass >> it to the reconstruction algorithm. In other words, if you use SimpleRTK, >> use ImageSeriesReader instead of ProjectionsReader. >> Regarding the geometry, it would be nice to be confident in the geometry >> parameters, maybe from their Matlab code? >> Simon >> >> >> On 21/01/2016 20:02, MG Vallet wrote: >> >> Hi Simon and Cyril, >> >> I really appreciate your insight. >> >> By examining the parameters of the acquisition, I saw that the center >> must effectively be offset (4.8 mm in both directions). For the attached >> image, I also increases sdd and sid by a factor 1000, just in case I would >> be wrong in units. It reduces the first default I pointed out in my first >> message. Also note that my input dataset was SophiaBeads_512_averaged. >> >> Regarding the pre-processing mentioned by Simon, I need more help. Is it >> as simple as the FDK filter assumes that the input is intensity, but the >> dataset provides -ln(I/I0) ? >> >> Regards, >> mg >> >> 2016-01-20 3:33 GMT-05:00 Simon Rit : >> >>> Hi, >>> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >>> is provided is directly the line integral. RTK will process the tif images >>> as if it were a photon count so I converted the tif projections to mha to >>> avoid this. For the conversion, I used another piece of software but you >>> can easily do the same thing with SimpleRTK. >>> Second, I used the enclosed script which gives me a much better result. >>> I have however a geometry problem. I think they provide a Matlab piece of >>> code to get the center of rotation. If you can run it and find out what is >>> this center, then you can use it to configure the geometry better with the >>> options --proj_iso_x and --proj_iso_y. >>> Good luck, >>> Simon >>> >>> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >>> mgvallet.pro at gmail.com> wrote: >>> >>>> Thanks Cyril! >>>> going to carefully check my inputs and I give you some news. >>>> mgv >>>> >>>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>>> cyril.mory at uclouvain.be>: >>>> >>>>> Hi, >>>>> >>>>> It looks like the geometry is wrong indeed, because I have never seen >>>>> such artifacts. >>>>> >>>>> Hope that helps, >>>>> Cyril >>>>> >>>>> >>>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>>> >>>>> Dear rtk-users, >>>>> >>>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>>> https://zenodo.org/record/16539. >>>>> This is a plastic tube filled with glass beads that has been scanned. >>>>> >>>>> Attached is a view of the reconstructed central slice. It is found >>>>> that: >>>>> >>>>> 1. the beads are quickly deformed outside the center >>>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>>> >>>>> My question is if these are simply expected artifacts. I am not 100% >>>>> sure I properly set the geometry parameters. >>>>> >>>>> Regards, >>>>> mgv >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> [image: Avast logo] >>>>> >>>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>>> logiciel antivirus Avast. >>>>> www.avast.com >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Jan 26 17:17:01 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 26 Jan 2016 23:17:01 +0100 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Hi MG, Sometimes, the progressive deformation from the center of rotation to the edge of the image is caused by wrong sdd/sid ratio. Such as change in the geometry will lead to distortion of the image and wrong magnification. Maybe you can play with that parameter and report your result. Cheers, Louie Sent from Mail for Windows 10 From: Simon Rit Sent: Tuesday, January 26, 2016 13:24 To: MG Vallet Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Sophia beads reconstruction Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and?ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was?SophiaBeads_512_averaged. Regarding the pre-processing?mentioned?by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit?: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from?https://zenodo.org/record/16539.? This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts.?I am not 100% sure I properly set the geometry parameters. Regards, mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. www.avast.com _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Thu Jan 28 16:27:15 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 28 Jan 2016 16:27:15 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: Louie, I played with sdd and sid, following your advise. But they have few effect, clearly less effect than proj_iso_x. And none of these parameters can significantly improve my result. Simon, I carefully checked every input data and I cant see what I did wrong. I want first to reproduce your output. You said earlier it's easy to convert a series of tiff image into a mha file using SimpleRTK. Do you mean by writing a short program, or is it possible from the command line ? MG 2016-01-26 17:17 GMT-05:00 louie L : > Hi MG, > > > > Sometimes, the progressive deformation from the center of rotation to the > edge of the image is caused by wrong sdd/sid ratio. Such as change in the > geometry will lead to distortion of the image and wrong magnification. > > Maybe you can play with that parameter and report your result. > > > > Cheers, > > Louie > > > > Sent from Mail for > Windows 10 > > > > > *From: *Simon Rit > *Sent: *Tuesday, January 26, 2016 13:24 > *To: *MG Vallet > *Cc: *rtk-users at public.kitware.com > *Subject: *Re: [Rtk-users] Sophia beads reconstruction > > > > Hi, > > I think it's likely a problem with parameters. The best would be to obtain > them from the Matlab code they provide. > > Good luck, > > Simon > > > > On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > > Hi Simon, > > > > this was a point I missed. I had to do the log mapping. > > > > I must say, I do not use RTK from shell. I just plugged the objects > > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > > > MG > > > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > > > I really appreciate your insight. > > > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > > > Regards, > > mg > > > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > > Hi, > > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > > Good luck, > > Simon > > > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > > Thanks Cyril! > > going to carefully check my inputs and I give you some news. > > mgv > > > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > > This is a plastic tube filled with glass beads that has been scanned. > > > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > > > Regards, > > mgv > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 4 16:55:56 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 4 Jan 2016 16:55:56 -0500 Subject: [Rtk-users] feldkamp application Message-ID: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Tue Jan 5 03:25:50 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 05 Jan 2016 09:25:50 +0100 Subject: [Rtk-users] feldkamp application In-Reply-To: References: Message-ID: <568B7E0E.9030904@uclouvain.be> Hi, and happy new year :) You can use the dataset provided for the motion-compensated reconstruction : http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Hope it helps, Cyril On 01/04/2016 10:55 PM, MG Vallet wrote: > Happy new year! > > Does someone have a data set, other than quadric phantoms, to test the > fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 5 05:16:50 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 5 Jan 2016 11:16:50 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: Message-ID: <568B9812.40404@creatis.insa-lyon.fr> Hi, I forgot to cc this email to the mailing list, in answers to mgv. Simon -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit To: MG Vallet Hi, There are vendor-specific examples available on the wiki: http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction You also have real patient data for 4D CBCT, e.g. http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Simon On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 5 16:50:09 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 5 Jan 2016 16:50:09 -0500 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: <568B9812.40404@creatis.insa-lyon.fr> References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: Thanks, Cyril and Simon. These applications seemed complicated to me, but it's only data reading that is. By the way, the command rtkfieldofview had no effect in the varian case (no error message, nor output file). Otherwise, everything's OK. 2016-01-05 5:16 GMT-05:00 Simon Rit : > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp > application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit > To: MG > Vallet > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet wrote: > >> Happy new year! >> >> Does someone have a data set, other than quadric phantoms, to test the >> fdk module ? >> It would be fine to add one to the wiki page >> http://wiki.openrtk.org/index.php/Main_Page#Applications >> >> mgv >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Mon Jan 11 09:34:58 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Mon, 11 Jan 2016 15:34:58 +0100 Subject: [Rtk-users] Parker weighting In-Reply-To: <56743FCB.3040102@creatis.insa-lyon.fr> References: <56667F38.6040604@creatis.insa-lyon.fr> <56743FCB.3040102@creatis.insa-lyon.fr> Message-ID: Dear Simon, I am sorry for the late reply. I also wish you a happy new year. I will recheck if there is any error during generating projection images. The projections are generated from a volume with our simulation tool. However, I generated projections from the volume with rtkforwardprojections and I re-reconstructed the volume with rtkfdk. I did not get any artifacts. I will contact you soon, if I have some results. Thank you very much for your help. Shiras On Fri, Dec 18, 2015 at 6:18 PM, Simon Rit wrote: > Hi Shiras, > Sorry for the delayed answer, times are busy. The way RTK computes the > spanned arc is from the second projection angle to the before last > projection angle, i.e., in your case > 209.609216488925-11.6067737022482 > so it's a span of 199 degrees and your cone angle is indeed too large. > Like I said, this part of RTK is perfectible and there is no way to change > this but change the code. > However, the source of artefacts might be something else. On simulated > data, I tried: > rtkprojectshepploganphantom --like original_proj.mhd -g > geometry_parker_corr.xml -o proj.mha > rtkfdk -p . -r proj.mha -o fdk.mha -g geometry_parker_corr.xml > and the result is not that bad. What do you think? Can you show us a > snapshot if sg's wrong in your opinion? > Simon > > > On 09/12/2015 11:01, Shiras Abdurahman wrote: > > Dear Simon, > > I am attaching the mhd files of projections. > > With regards, > Shiras > > On Tue, Dec 8, 2015 at 6:17 PM, Simon Rit > wrote: > >> Hi, >> The geometry files look ok to me. What is the projection information? If >> you're still getting the same message as before, I think it's because you >> don't have enough data. If you send the mhd file of the projections (just >> the mhd, not the raw data), I can try to test it on simulated data to let >> you know my feeling. >> Simon >> >> On Tue, Dec 8, 2015 at 5:41 PM, Shiras Abdurahman < >> shiraska at gmail.com> wrote: >> >>> Dear Simon, >>> >>> I tried this option and unfortunately it did not work. I added zero >>> projections and modified geometry files. However, I am getting same >>> artifacts in the volume. Voxel values changed a little bit that indicates >>> during backprojection it still considers extreme projections. I am also >>> getting an output message same as before. >>> >>> I am attaching geometry files. >>> >>> With regards, >>> Shiras >>> >>> On Tue, Dec 8, 2015 at 10:15 AM, Simon Rit < >>> simon.rit at creatis.insa-lyon.fr> wrote: >>> >>>> So calling AddProjection before and after the loop with an adequate >>>> gantry_angle should work. >>>> Simon >>>> >>>> On Tue, Dec 8, 2015 at 9:52 AM, Shiras Abdurahman < >>>> shiraska at gmail.com> wrote: >>>> >>>>> Drear Simon, >>>>> >>>>> I generate the geometry with system geometry parameters and using >>>>> AddProjection method. >>>>> >>>>> Here is the code >>>>> >>>>> >>>>> rtk::ThreeDCircularProjectionGeometry::Pointer rtk_sys_geometry_; >>>>> rtk_sys_geometry_ = rtk::ThreeDCircularProjectionGeometry::New(); >>>>> for (uint16_t proj_index = 0; proj_index < num_projections_; >>>>> proj_index++) >>>>> { >>>>> >>>>> rtk_sys_geometry_->AddProjection(rtk_geom_params_.at(proj_index).sid_mm, >>>>> rtk_geom_params_.at(proj_index).sdd_mm, >>>>> rtk_geom_params_.at(proj_index).gantry_angle_deg, >>>>> rtk_geom_params_.at(proj_index).proj_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).proj_offset_y_mm, >>>>> rtk_geom_params_.at(proj_index).out_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).in_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).src_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).src_offset_y_mm); >>>>> } >>>>> >>>>> And then write to xml file. >>>>> >>>>> Shiras >>>>> >>>>> >>>>> >>>>> On Tue, Dec 8, 2015 at 9:23 AM, Simon Rit < >>>>> simon.rit at creatis.insa-lyon.fr> wrote: >>>>> >>>>>> Hi, >>>>>> rtkfdk.cxx just read the geometry from a file so the best is to >>>>>> modify the geometry file. How do you generate the geometry? >>>>>> For example, if you use rtksimulated geometry, let's say that you >>>>>> were using: >>>>>> rtksimulatedgeometry -n 200 -a 200 -o g.xml >>>>>> then you'll have to replace it with >>>>>> rtksimulatedgeometry -n 202 -a 202 -o g.xml -f -1 >>>>>> Don't forget to add dummy projection at the beginning and the end. If >>>>>> you use a more complex geometry, maybe SimpleRTK >>>>>> can be helpful >>>>>> (I'd use that) or you'd have to modify the cxx code to add these additional >>>>>> projections in the geometry and the projection stack. >>>>>> Simon >>>>>> >>>>>> >>>>>> On Tue, Dec 8, 2015 at 8:51 AM, Shiras Abdurahman < >>>>>> shiraska at gmail.com> wrote: >>>>>> >>>>>>> Dear Simon, >>>>>>> >>>>>>> Thanks a lot for the reply. Can you please inform me how can I set >>>>>>> where the arc starts? >>>>>>> Do I need to modify geometry also? >>>>>>> If you can point the line of code rtkfdk.cxx, it will be really >>>>>>> helpful. >>>>>>> >>>>>>> With regards, >>>>>>> Shiras >>>>>>> >>>>>>> On Tue, Dec 8, 2015 at 7:56 AM, Simon Rit < >>>>>>> simon.rit at creatis.insa-lyon.fr> >>>>>>> wrote: >>>>>>> >>>>>>>> Dear Shiras, >>>>>>>> Yes, for practical reasons the first and the last projections are >>>>>>>> set to 0 and the arc used in the Parker weighting starts between the first >>>>>>>> two projections and ends between the lasts two projections. There is a >>>>>>>> simple solution: add a projection at the beginning and the end of the arc, >>>>>>>> which can contain any pixel values but should be set where you want this >>>>>>>> arc to start. In the future, I think someone should once take the time to >>>>>>>> correct this but I haven't so far. I'll keep you posted on the mailing list >>>>>>>> when it's corrected. >>>>>>>> Simon >>>>>>>> >>>>>>>> On 07/12/2015 12:04, Shiras Abdurahman wrote: >>>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I am trying to reconstruct a volume from projection data generated >>>>>>>> with C-arm CT. There are 248 projections with an angular range of 199 >>>>>>>> degree. Technically, parker weighting should run without any problems. >>>>>>>> However, I am getting an output message that "You do not have enough data >>>>>>>> for proper parker weighting". After parker weighting, the two extreme >>>>>>>> projections (projection number 1 and 248) were completely zero and thus >>>>>>>> reconstructed volume contained artifacts. When I increased the angular >>>>>>>> range, this problem did not happen. How can I solve this problem without >>>>>>>> increasing angular range? Is there any threshold constant that I can change >>>>>>>> in command line or in my code? >>>>>>>> >>>>>>>> I really appreciate any help you can provide. >>>>>>>> >>>>>>>> With regards, >>>>>>>> Shiras >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 12 07:47:46 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 12 Jan 2016 13:47:46 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: <5694F5F2.4060702@creatis.insa-lyon.fr> Hi, There was a typo on the folder path (../Scan0 instead of Scan0). Was that the problem? I checked and it has the expected effect, i.e., setting to 0 everything outside the FOV. Simon On 05/01/2016 22:50, MG Vallet wrote: > Thanks, Cyril and Simon. > These applications seemed complicated to me, but it's only data > reading that is. > By the way, the command rtkfieldofview had no effect in the varian > case (no error message, nor output file). Otherwise, everything's OK. > > 2016-01-05 5:16 GMT-05:00 Simon Rit >: > > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- > Subject: Re: [Rtk-users] feldkamp application > Date: Tue, 5 Jan 2016 08:40:00 +0100 > From: Simon Rit > > To: MG Vallet > > > > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: > > Happy new year! > > Does someone have a data set, other than quadric phantoms, to > test the fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Wed Jan 13 07:42:45 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Wed, 13 Jan 2016 13:42:45 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry Message-ID: Dear all, I am trying to generate geometry xml file with rtkReg23ProjectionGeometry after decomposing projection matrix. One of the argument to the function AddReg23Projection is detector position. I assume that, it is the position vector of the center of the first pixel in world co-ordinates. This will be used for computing the projection offset parameters by projecting detector origin vector onto the u and v axis of the detector. If that is the case, do we need to change the offset parameters of each projection in the mhd file. Will this create problems during displaced detector correction? With regards, Shiras -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 13 13:31:23 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Jan 2016 19:31:23 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry In-Reply-To: References: Message-ID: <569697FB.1020804@creatis.insa-lyon.fr> Hi, Wrong assumption. It's the coordinate of point (0,0) in the coordinate of the projection image in the word coordinates, it's not the coordinate of the center of the first pixel. This is mentioned in the geometry description file on the wiki. You should not change the mhd parameters. If you want to account for offset parameters that change from projection to projection, you can put that offset in the computation of the detector position in world coordinates. Simon On 13/01/2016 13:42, Shiras Abdurahman wrote: > Dear all, > > I am trying to generate geometry xml file with > rtkReg23ProjectionGeometry after decomposing projection matrix. One of > the argument to the function AddReg23Projection is detector position. > I assume that, it is the position vector of the center of the first > pixel in world co-ordinates. This will be used for computing the > projection offset parameters by projecting detector origin vector onto > the u and v axis of the detector. If that is the case, do we need to > change the offset parameters of each projection in the mhd file. Will > this create problems during displaced detector correction? > > > With regards, > Shiras > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 10:19:12 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 10:19:12 -0500 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from https://zenodo.org/record/16539. This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts. I am not 100% sure I properly set the geometry parameters. Regards, mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sophiaBeadsCentralSlide.jpg Type: image/jpeg Size: 55394 bytes Desc: not available URL: From cyril.mory at uclouvain.be Tue Jan 19 10:33:02 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 19 Jan 2016 16:33:02 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: <569E572E.20203@uclouvain.be> Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit : > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% > sure I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users --- L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 14:02:45 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 14:02:45 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <569E572E.20203@uclouvain.be> References: <569E572E.20203@uclouvain.be> Message-ID: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > > ------------------------------ > [image: Avast logo] > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 20 03:33:47 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 20 Jan 2016 09:33:47 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > >> Hi, >> >> It looks like the geometry is wrong indeed, because I have never seen >> such artifacts. >> >> Hope that helps, >> Cyril >> >> >> Le 19/01/2016 16:19, MG Vallet a ?crit : >> >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data set from >> https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has been scanned. >> >> Attached is a view of the reconstructed central slice. It is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the proper term) >> >> My question is if these are simply expected artifacts. I am not 100% >> sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> >> ------------------------------ >> [image: Avast logo] >> >> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >> logiciel antivirus Avast. >> www.avast.com >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkfdk.sh Type: application/x-sh Size: 404 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: snapshot.jpg Type: image/jpeg Size: 95222 bytes Desc: not available URL: From mgvallet.pro at gmail.com Thu Jan 21 14:02:28 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 21 Jan 2016 14:02:28 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was SophiaBeads_512_averaged. Regarding the pre-processing mentioned by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > >> Thanks Cyril! >> going to carefully check my inputs and I give you some news. >> mgv >> >> 2016-01-19 10:33 GMT-05:00 Cyril Mory : >> >>> Hi, >>> >>> It looks like the geometry is wrong indeed, because I have never seen >>> such artifacts. >>> >>> Hope that helps, >>> Cyril >>> >>> >>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>> >>> Dear rtk-users, >>> >>> I applied the FDKConeBeamReconstructionFilter to a data set from >>> https://zenodo.org/record/16539. >>> This is a plastic tube filled with glass beads that has been scanned. >>> >>> Attached is a view of the reconstructed central slice. It is found that: >>> >>> 1. the beads are quickly deformed outside the center >>> 2. each one has a halo, or a shadow (dont know the proper term) >>> >>> My question is if these are simply expected artifacts. I am not 100% >>> sure I properly set the geometry parameters. >>> >>> Regards, >>> mgv >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >>> >>> ------------------------------ >>> [image: Avast logo] >>> >>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>> logiciel antivirus Avast. >>> www.avast.com >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_offset.jpg Type: image/jpeg Size: 52844 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Thu Jan 21 14:22:55 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Jan 2016 20:22:55 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: <56A1300F.1090509@creatis.insa-lyon.fr> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center > must effectively be offset (4.8 mm in both directions). For the > attached image, I also increases sdd and sid by a factor 1000, just in > case I would be wrong in units. It reduces the first default I pointed > out in my first message. Also note that my input dataset was > SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is > it as simple as the FDK filter assumes that the input is intensity, > but the dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit >: > > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems > that what is provided is directly the line integral. RTK will > process the tif images as if it were a photon count so I converted > the tif projections to mha to avoid this. For the conversion, I > used another piece of software but you can easily do the same > thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better > result. I have however a geometry problem. I think they provide a > Matlab piece of code to get the center of rotation. If you can run > it and find out what is this center, then you can use it to > configure the geometry better with the options --proj_iso_x and > --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet > wrote: > > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory >: > > Hi, > > It looks like the geometry is wrong indeed, because I have > never seen such artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data >> set from https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has >> been scanned. >> >> Attached is a view of the reconstructed central slice. It >> is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the >> proper term) >> >> My question is if these are simply expected artifacts. I >> am not 100% sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> >> http://public.kitware.com/mailman/listinfo/rtk-users > > > > ------------------------------------------------------------------------ > Avast logo > > L'absence de virus dans ce courrier ?lectronique a ?t? > v?rifi?e par le logiciel antivirus Avast. > www.avast.com > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 25 11:48:35 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 25 Jan 2016 11:48:35 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <56A1300F.1090509@creatis.insa-lyon.fr> References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > >> Hi, >> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >> is provided is directly the line integral. RTK will process the tif images >> as if it were a photon count so I converted the tif projections to mha to >> avoid this. For the conversion, I used another piece of software but you >> can easily do the same thing with SimpleRTK. >> Second, I used the enclosed script which gives me a much better result. I >> have however a geometry problem. I think they provide a Matlab piece of >> code to get the center of rotation. If you can run it and find out what is >> this center, then you can use it to configure the geometry better with the >> options --proj_iso_x and --proj_iso_y. >> Good luck, >> Simon >> >> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >> mgvallet.pro at gmail.com> wrote: >> >>> Thanks Cyril! >>> going to carefully check my inputs and I give you some news. >>> mgv >>> >>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>> cyril.mory at uclouvain.be>: >>> >>>> Hi, >>>> >>>> It looks like the geometry is wrong indeed, because I have never seen >>>> such artifacts. >>>> >>>> Hope that helps, >>>> Cyril >>>> >>>> >>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>> >>>> Dear rtk-users, >>>> >>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>> https://zenodo.org/record/16539. >>>> This is a plastic tube filled with glass beads that has been scanned. >>>> >>>> Attached is a view of the reconstructed central slice. It is found that: >>>> >>>> 1. the beads are quickly deformed outside the center >>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>> >>>> My question is if these are simply expected artifacts. I am not 100% >>>> sure I properly set the geometry parameters. >>>> >>>> Regards, >>>> mgv >>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> [image: Avast logo] >>>> >>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>> logiciel antivirus Avast. >>>> www.avast.com >>>> >>>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_log.jpg Type: image/jpeg Size: 17331 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 26 07:23:58 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Jan 2016 13:23:58 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > Hi Simon, > > this was a point I missed. I had to do the log mapping. > > I must say, I do not use RTK from shell. I just plugged the objects > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > MG > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > >> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the >> line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the >> projections and converts them depending on the type: for mha or mhd, it >> just reads it and nothing else. For tif, it assumes that I is passed, try >> to guess I0 (or gets it from the cmd line) and computes ln(I0/I). >> So from each tif projection, instead of letting them go through the >> ProjectionsReader in RTK, directly use the ImageReader, stack them and pass >> it to the reconstruction algorithm. In other words, if you use SimpleRTK, >> use ImageSeriesReader instead of ProjectionsReader. >> Regarding the geometry, it would be nice to be confident in the geometry >> parameters, maybe from their Matlab code? >> Simon >> >> >> On 21/01/2016 20:02, MG Vallet wrote: >> >> Hi Simon and Cyril, >> >> I really appreciate your insight. >> >> By examining the parameters of the acquisition, I saw that the center >> must effectively be offset (4.8 mm in both directions). For the attached >> image, I also increases sdd and sid by a factor 1000, just in case I would >> be wrong in units. It reduces the first default I pointed out in my first >> message. Also note that my input dataset was SophiaBeads_512_averaged. >> >> Regarding the pre-processing mentioned by Simon, I need more help. Is it >> as simple as the FDK filter assumes that the input is intensity, but the >> dataset provides -ln(I/I0) ? >> >> Regards, >> mg >> >> 2016-01-20 3:33 GMT-05:00 Simon Rit : >> >>> Hi, >>> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >>> is provided is directly the line integral. RTK will process the tif images >>> as if it were a photon count so I converted the tif projections to mha to >>> avoid this. For the conversion, I used another piece of software but you >>> can easily do the same thing with SimpleRTK. >>> Second, I used the enclosed script which gives me a much better result. >>> I have however a geometry problem. I think they provide a Matlab piece of >>> code to get the center of rotation. If you can run it and find out what is >>> this center, then you can use it to configure the geometry better with the >>> options --proj_iso_x and --proj_iso_y. >>> Good luck, >>> Simon >>> >>> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >>> mgvallet.pro at gmail.com> wrote: >>> >>>> Thanks Cyril! >>>> going to carefully check my inputs and I give you some news. >>>> mgv >>>> >>>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>>> cyril.mory at uclouvain.be>: >>>> >>>>> Hi, >>>>> >>>>> It looks like the geometry is wrong indeed, because I have never seen >>>>> such artifacts. >>>>> >>>>> Hope that helps, >>>>> Cyril >>>>> >>>>> >>>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>>> >>>>> Dear rtk-users, >>>>> >>>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>>> https://zenodo.org/record/16539. >>>>> This is a plastic tube filled with glass beads that has been scanned. >>>>> >>>>> Attached is a view of the reconstructed central slice. It is found >>>>> that: >>>>> >>>>> 1. the beads are quickly deformed outside the center >>>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>>> >>>>> My question is if these are simply expected artifacts. I am not 100% >>>>> sure I properly set the geometry parameters. >>>>> >>>>> Regards, >>>>> mgv >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> [image: Avast logo] >>>>> >>>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>>> logiciel antivirus Avast. >>>>> www.avast.com >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Jan 26 17:17:01 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 26 Jan 2016 23:17:01 +0100 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Hi MG, Sometimes, the progressive deformation from the center of rotation to the edge of the image is caused by wrong sdd/sid ratio. Such as change in the geometry will lead to distortion of the image and wrong magnification. Maybe you can play with that parameter and report your result. Cheers, Louie Sent from Mail for Windows 10 From: Simon Rit Sent: Tuesday, January 26, 2016 13:24 To: MG Vallet Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Sophia beads reconstruction Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and?ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was?SophiaBeads_512_averaged. Regarding the pre-processing?mentioned?by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit?: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from?https://zenodo.org/record/16539.? This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts.?I am not 100% sure I properly set the geometry parameters. Regards, mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. www.avast.com _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Thu Jan 28 16:27:15 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 28 Jan 2016 16:27:15 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: Louie, I played with sdd and sid, following your advise. But they have few effect, clearly less effect than proj_iso_x. And none of these parameters can significantly improve my result. Simon, I carefully checked every input data and I cant see what I did wrong. I want first to reproduce your output. You said earlier it's easy to convert a series of tiff image into a mha file using SimpleRTK. Do you mean by writing a short program, or is it possible from the command line ? MG 2016-01-26 17:17 GMT-05:00 louie L : > Hi MG, > > > > Sometimes, the progressive deformation from the center of rotation to the > edge of the image is caused by wrong sdd/sid ratio. Such as change in the > geometry will lead to distortion of the image and wrong magnification. > > Maybe you can play with that parameter and report your result. > > > > Cheers, > > Louie > > > > Sent from Mail for > Windows 10 > > > > > *From: *Simon Rit > *Sent: *Tuesday, January 26, 2016 13:24 > *To: *MG Vallet > *Cc: *rtk-users at public.kitware.com > *Subject: *Re: [Rtk-users] Sophia beads reconstruction > > > > Hi, > > I think it's likely a problem with parameters. The best would be to obtain > them from the Matlab code they provide. > > Good luck, > > Simon > > > > On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > > Hi Simon, > > > > this was a point I missed. I had to do the log mapping. > > > > I must say, I do not use RTK from shell. I just plugged the objects > > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > > > MG > > > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > > > I really appreciate your insight. > > > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > > > Regards, > > mg > > > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > > Hi, > > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > > Good luck, > > Simon > > > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > > Thanks Cyril! > > going to carefully check my inputs and I give you some news. > > mgv > > > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > > This is a plastic tube filled with glass beads that has been scanned. > > > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > > > Regards, > > mgv > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 4 16:55:56 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 4 Jan 2016 16:55:56 -0500 Subject: [Rtk-users] feldkamp application Message-ID: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Tue Jan 5 03:25:50 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 05 Jan 2016 09:25:50 +0100 Subject: [Rtk-users] feldkamp application In-Reply-To: References: Message-ID: <568B7E0E.9030904@uclouvain.be> Hi, and happy new year :) You can use the dataset provided for the motion-compensated reconstruction : http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Hope it helps, Cyril On 01/04/2016 10:55 PM, MG Vallet wrote: > Happy new year! > > Does someone have a data set, other than quadric phantoms, to test the > fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 5 05:16:50 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 5 Jan 2016 11:16:50 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: Message-ID: <568B9812.40404@creatis.insa-lyon.fr> Hi, I forgot to cc this email to the mailing list, in answers to mgv. Simon -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit To: MG Vallet Hi, There are vendor-specific examples available on the wiki: http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction You also have real patient data for 4D CBCT, e.g. http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Simon On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 5 16:50:09 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 5 Jan 2016 16:50:09 -0500 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: <568B9812.40404@creatis.insa-lyon.fr> References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: Thanks, Cyril and Simon. These applications seemed complicated to me, but it's only data reading that is. By the way, the command rtkfieldofview had no effect in the varian case (no error message, nor output file). Otherwise, everything's OK. 2016-01-05 5:16 GMT-05:00 Simon Rit : > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp > application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit > To: MG > Vallet > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet wrote: > >> Happy new year! >> >> Does someone have a data set, other than quadric phantoms, to test the >> fdk module ? >> It would be fine to add one to the wiki page >> http://wiki.openrtk.org/index.php/Main_Page#Applications >> >> mgv >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Mon Jan 11 09:34:58 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Mon, 11 Jan 2016 15:34:58 +0100 Subject: [Rtk-users] Parker weighting In-Reply-To: <56743FCB.3040102@creatis.insa-lyon.fr> References: <56667F38.6040604@creatis.insa-lyon.fr> <56743FCB.3040102@creatis.insa-lyon.fr> Message-ID: Dear Simon, I am sorry for the late reply. I also wish you a happy new year. I will recheck if there is any error during generating projection images. The projections are generated from a volume with our simulation tool. However, I generated projections from the volume with rtkforwardprojections and I re-reconstructed the volume with rtkfdk. I did not get any artifacts. I will contact you soon, if I have some results. Thank you very much for your help. Shiras On Fri, Dec 18, 2015 at 6:18 PM, Simon Rit wrote: > Hi Shiras, > Sorry for the delayed answer, times are busy. The way RTK computes the > spanned arc is from the second projection angle to the before last > projection angle, i.e., in your case > 209.609216488925-11.6067737022482 > so it's a span of 199 degrees and your cone angle is indeed too large. > Like I said, this part of RTK is perfectible and there is no way to change > this but change the code. > However, the source of artefacts might be something else. On simulated > data, I tried: > rtkprojectshepploganphantom --like original_proj.mhd -g > geometry_parker_corr.xml -o proj.mha > rtkfdk -p . -r proj.mha -o fdk.mha -g geometry_parker_corr.xml > and the result is not that bad. What do you think? Can you show us a > snapshot if sg's wrong in your opinion? > Simon > > > On 09/12/2015 11:01, Shiras Abdurahman wrote: > > Dear Simon, > > I am attaching the mhd files of projections. > > With regards, > Shiras > > On Tue, Dec 8, 2015 at 6:17 PM, Simon Rit > wrote: > >> Hi, >> The geometry files look ok to me. What is the projection information? If >> you're still getting the same message as before, I think it's because you >> don't have enough data. If you send the mhd file of the projections (just >> the mhd, not the raw data), I can try to test it on simulated data to let >> you know my feeling. >> Simon >> >> On Tue, Dec 8, 2015 at 5:41 PM, Shiras Abdurahman < >> shiraska at gmail.com> wrote: >> >>> Dear Simon, >>> >>> I tried this option and unfortunately it did not work. I added zero >>> projections and modified geometry files. However, I am getting same >>> artifacts in the volume. Voxel values changed a little bit that indicates >>> during backprojection it still considers extreme projections. I am also >>> getting an output message same as before. >>> >>> I am attaching geometry files. >>> >>> With regards, >>> Shiras >>> >>> On Tue, Dec 8, 2015 at 10:15 AM, Simon Rit < >>> simon.rit at creatis.insa-lyon.fr> wrote: >>> >>>> So calling AddProjection before and after the loop with an adequate >>>> gantry_angle should work. >>>> Simon >>>> >>>> On Tue, Dec 8, 2015 at 9:52 AM, Shiras Abdurahman < >>>> shiraska at gmail.com> wrote: >>>> >>>>> Drear Simon, >>>>> >>>>> I generate the geometry with system geometry parameters and using >>>>> AddProjection method. >>>>> >>>>> Here is the code >>>>> >>>>> >>>>> rtk::ThreeDCircularProjectionGeometry::Pointer rtk_sys_geometry_; >>>>> rtk_sys_geometry_ = rtk::ThreeDCircularProjectionGeometry::New(); >>>>> for (uint16_t proj_index = 0; proj_index < num_projections_; >>>>> proj_index++) >>>>> { >>>>> >>>>> rtk_sys_geometry_->AddProjection(rtk_geom_params_.at(proj_index).sid_mm, >>>>> rtk_geom_params_.at(proj_index).sdd_mm, >>>>> rtk_geom_params_.at(proj_index).gantry_angle_deg, >>>>> rtk_geom_params_.at(proj_index).proj_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).proj_offset_y_mm, >>>>> rtk_geom_params_.at(proj_index).out_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).in_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).src_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).src_offset_y_mm); >>>>> } >>>>> >>>>> And then write to xml file. >>>>> >>>>> Shiras >>>>> >>>>> >>>>> >>>>> On Tue, Dec 8, 2015 at 9:23 AM, Simon Rit < >>>>> simon.rit at creatis.insa-lyon.fr> wrote: >>>>> >>>>>> Hi, >>>>>> rtkfdk.cxx just read the geometry from a file so the best is to >>>>>> modify the geometry file. How do you generate the geometry? >>>>>> For example, if you use rtksimulated geometry, let's say that you >>>>>> were using: >>>>>> rtksimulatedgeometry -n 200 -a 200 -o g.xml >>>>>> then you'll have to replace it with >>>>>> rtksimulatedgeometry -n 202 -a 202 -o g.xml -f -1 >>>>>> Don't forget to add dummy projection at the beginning and the end. If >>>>>> you use a more complex geometry, maybe SimpleRTK >>>>>> can be helpful >>>>>> (I'd use that) or you'd have to modify the cxx code to add these additional >>>>>> projections in the geometry and the projection stack. >>>>>> Simon >>>>>> >>>>>> >>>>>> On Tue, Dec 8, 2015 at 8:51 AM, Shiras Abdurahman < >>>>>> shiraska at gmail.com> wrote: >>>>>> >>>>>>> Dear Simon, >>>>>>> >>>>>>> Thanks a lot for the reply. Can you please inform me how can I set >>>>>>> where the arc starts? >>>>>>> Do I need to modify geometry also? >>>>>>> If you can point the line of code rtkfdk.cxx, it will be really >>>>>>> helpful. >>>>>>> >>>>>>> With regards, >>>>>>> Shiras >>>>>>> >>>>>>> On Tue, Dec 8, 2015 at 7:56 AM, Simon Rit < >>>>>>> simon.rit at creatis.insa-lyon.fr> >>>>>>> wrote: >>>>>>> >>>>>>>> Dear Shiras, >>>>>>>> Yes, for practical reasons the first and the last projections are >>>>>>>> set to 0 and the arc used in the Parker weighting starts between the first >>>>>>>> two projections and ends between the lasts two projections. There is a >>>>>>>> simple solution: add a projection at the beginning and the end of the arc, >>>>>>>> which can contain any pixel values but should be set where you want this >>>>>>>> arc to start. In the future, I think someone should once take the time to >>>>>>>> correct this but I haven't so far. I'll keep you posted on the mailing list >>>>>>>> when it's corrected. >>>>>>>> Simon >>>>>>>> >>>>>>>> On 07/12/2015 12:04, Shiras Abdurahman wrote: >>>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I am trying to reconstruct a volume from projection data generated >>>>>>>> with C-arm CT. There are 248 projections with an angular range of 199 >>>>>>>> degree. Technically, parker weighting should run without any problems. >>>>>>>> However, I am getting an output message that "You do not have enough data >>>>>>>> for proper parker weighting". After parker weighting, the two extreme >>>>>>>> projections (projection number 1 and 248) were completely zero and thus >>>>>>>> reconstructed volume contained artifacts. When I increased the angular >>>>>>>> range, this problem did not happen. How can I solve this problem without >>>>>>>> increasing angular range? Is there any threshold constant that I can change >>>>>>>> in command line or in my code? >>>>>>>> >>>>>>>> I really appreciate any help you can provide. >>>>>>>> >>>>>>>> With regards, >>>>>>>> Shiras >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 12 07:47:46 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 12 Jan 2016 13:47:46 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: <5694F5F2.4060702@creatis.insa-lyon.fr> Hi, There was a typo on the folder path (../Scan0 instead of Scan0). Was that the problem? I checked and it has the expected effect, i.e., setting to 0 everything outside the FOV. Simon On 05/01/2016 22:50, MG Vallet wrote: > Thanks, Cyril and Simon. > These applications seemed complicated to me, but it's only data > reading that is. > By the way, the command rtkfieldofview had no effect in the varian > case (no error message, nor output file). Otherwise, everything's OK. > > 2016-01-05 5:16 GMT-05:00 Simon Rit >: > > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- > Subject: Re: [Rtk-users] feldkamp application > Date: Tue, 5 Jan 2016 08:40:00 +0100 > From: Simon Rit > > To: MG Vallet > > > > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: > > Happy new year! > > Does someone have a data set, other than quadric phantoms, to > test the fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Wed Jan 13 07:42:45 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Wed, 13 Jan 2016 13:42:45 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry Message-ID: Dear all, I am trying to generate geometry xml file with rtkReg23ProjectionGeometry after decomposing projection matrix. One of the argument to the function AddReg23Projection is detector position. I assume that, it is the position vector of the center of the first pixel in world co-ordinates. This will be used for computing the projection offset parameters by projecting detector origin vector onto the u and v axis of the detector. If that is the case, do we need to change the offset parameters of each projection in the mhd file. Will this create problems during displaced detector correction? With regards, Shiras -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 13 13:31:23 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Jan 2016 19:31:23 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry In-Reply-To: References: Message-ID: <569697FB.1020804@creatis.insa-lyon.fr> Hi, Wrong assumption. It's the coordinate of point (0,0) in the coordinate of the projection image in the word coordinates, it's not the coordinate of the center of the first pixel. This is mentioned in the geometry description file on the wiki. You should not change the mhd parameters. If you want to account for offset parameters that change from projection to projection, you can put that offset in the computation of the detector position in world coordinates. Simon On 13/01/2016 13:42, Shiras Abdurahman wrote: > Dear all, > > I am trying to generate geometry xml file with > rtkReg23ProjectionGeometry after decomposing projection matrix. One of > the argument to the function AddReg23Projection is detector position. > I assume that, it is the position vector of the center of the first > pixel in world co-ordinates. This will be used for computing the > projection offset parameters by projecting detector origin vector onto > the u and v axis of the detector. If that is the case, do we need to > change the offset parameters of each projection in the mhd file. Will > this create problems during displaced detector correction? > > > With regards, > Shiras > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 10:19:12 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 10:19:12 -0500 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from https://zenodo.org/record/16539. This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts. I am not 100% sure I properly set the geometry parameters. Regards, mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sophiaBeadsCentralSlide.jpg Type: image/jpeg Size: 55394 bytes Desc: not available URL: From cyril.mory at uclouvain.be Tue Jan 19 10:33:02 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 19 Jan 2016 16:33:02 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: <569E572E.20203@uclouvain.be> Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit : > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% > sure I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users --- L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 14:02:45 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 14:02:45 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <569E572E.20203@uclouvain.be> References: <569E572E.20203@uclouvain.be> Message-ID: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > > ------------------------------ > [image: Avast logo] > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 20 03:33:47 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 20 Jan 2016 09:33:47 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > >> Hi, >> >> It looks like the geometry is wrong indeed, because I have never seen >> such artifacts. >> >> Hope that helps, >> Cyril >> >> >> Le 19/01/2016 16:19, MG Vallet a ?crit : >> >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data set from >> https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has been scanned. >> >> Attached is a view of the reconstructed central slice. It is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the proper term) >> >> My question is if these are simply expected artifacts. I am not 100% >> sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> >> ------------------------------ >> [image: Avast logo] >> >> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >> logiciel antivirus Avast. >> www.avast.com >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkfdk.sh Type: application/x-sh Size: 404 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: snapshot.jpg Type: image/jpeg Size: 95222 bytes Desc: not available URL: From mgvallet.pro at gmail.com Thu Jan 21 14:02:28 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 21 Jan 2016 14:02:28 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was SophiaBeads_512_averaged. Regarding the pre-processing mentioned by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > >> Thanks Cyril! >> going to carefully check my inputs and I give you some news. >> mgv >> >> 2016-01-19 10:33 GMT-05:00 Cyril Mory : >> >>> Hi, >>> >>> It looks like the geometry is wrong indeed, because I have never seen >>> such artifacts. >>> >>> Hope that helps, >>> Cyril >>> >>> >>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>> >>> Dear rtk-users, >>> >>> I applied the FDKConeBeamReconstructionFilter to a data set from >>> https://zenodo.org/record/16539. >>> This is a plastic tube filled with glass beads that has been scanned. >>> >>> Attached is a view of the reconstructed central slice. It is found that: >>> >>> 1. the beads are quickly deformed outside the center >>> 2. each one has a halo, or a shadow (dont know the proper term) >>> >>> My question is if these are simply expected artifacts. I am not 100% >>> sure I properly set the geometry parameters. >>> >>> Regards, >>> mgv >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >>> >>> ------------------------------ >>> [image: Avast logo] >>> >>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>> logiciel antivirus Avast. >>> www.avast.com >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_offset.jpg Type: image/jpeg Size: 52844 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Thu Jan 21 14:22:55 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Jan 2016 20:22:55 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: <56A1300F.1090509@creatis.insa-lyon.fr> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center > must effectively be offset (4.8 mm in both directions). For the > attached image, I also increases sdd and sid by a factor 1000, just in > case I would be wrong in units. It reduces the first default I pointed > out in my first message. Also note that my input dataset was > SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is > it as simple as the FDK filter assumes that the input is intensity, > but the dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit >: > > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems > that what is provided is directly the line integral. RTK will > process the tif images as if it were a photon count so I converted > the tif projections to mha to avoid this. For the conversion, I > used another piece of software but you can easily do the same > thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better > result. I have however a geometry problem. I think they provide a > Matlab piece of code to get the center of rotation. If you can run > it and find out what is this center, then you can use it to > configure the geometry better with the options --proj_iso_x and > --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet > wrote: > > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory >: > > Hi, > > It looks like the geometry is wrong indeed, because I have > never seen such artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data >> set from https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has >> been scanned. >> >> Attached is a view of the reconstructed central slice. It >> is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the >> proper term) >> >> My question is if these are simply expected artifacts. I >> am not 100% sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> >> http://public.kitware.com/mailman/listinfo/rtk-users > > > > ------------------------------------------------------------------------ > Avast logo > > L'absence de virus dans ce courrier ?lectronique a ?t? > v?rifi?e par le logiciel antivirus Avast. > www.avast.com > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 25 11:48:35 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 25 Jan 2016 11:48:35 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <56A1300F.1090509@creatis.insa-lyon.fr> References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > >> Hi, >> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >> is provided is directly the line integral. RTK will process the tif images >> as if it were a photon count so I converted the tif projections to mha to >> avoid this. For the conversion, I used another piece of software but you >> can easily do the same thing with SimpleRTK. >> Second, I used the enclosed script which gives me a much better result. I >> have however a geometry problem. I think they provide a Matlab piece of >> code to get the center of rotation. If you can run it and find out what is >> this center, then you can use it to configure the geometry better with the >> options --proj_iso_x and --proj_iso_y. >> Good luck, >> Simon >> >> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >> mgvallet.pro at gmail.com> wrote: >> >>> Thanks Cyril! >>> going to carefully check my inputs and I give you some news. >>> mgv >>> >>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>> cyril.mory at uclouvain.be>: >>> >>>> Hi, >>>> >>>> It looks like the geometry is wrong indeed, because I have never seen >>>> such artifacts. >>>> >>>> Hope that helps, >>>> Cyril >>>> >>>> >>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>> >>>> Dear rtk-users, >>>> >>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>> https://zenodo.org/record/16539. >>>> This is a plastic tube filled with glass beads that has been scanned. >>>> >>>> Attached is a view of the reconstructed central slice. It is found that: >>>> >>>> 1. the beads are quickly deformed outside the center >>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>> >>>> My question is if these are simply expected artifacts. I am not 100% >>>> sure I properly set the geometry parameters. >>>> >>>> Regards, >>>> mgv >>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> [image: Avast logo] >>>> >>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>> logiciel antivirus Avast. >>>> www.avast.com >>>> >>>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_log.jpg Type: image/jpeg Size: 17331 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 26 07:23:58 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Jan 2016 13:23:58 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > Hi Simon, > > this was a point I missed. I had to do the log mapping. > > I must say, I do not use RTK from shell. I just plugged the objects > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > MG > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > >> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the >> line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the >> projections and converts them depending on the type: for mha or mhd, it >> just reads it and nothing else. For tif, it assumes that I is passed, try >> to guess I0 (or gets it from the cmd line) and computes ln(I0/I). >> So from each tif projection, instead of letting them go through the >> ProjectionsReader in RTK, directly use the ImageReader, stack them and pass >> it to the reconstruction algorithm. In other words, if you use SimpleRTK, >> use ImageSeriesReader instead of ProjectionsReader. >> Regarding the geometry, it would be nice to be confident in the geometry >> parameters, maybe from their Matlab code? >> Simon >> >> >> On 21/01/2016 20:02, MG Vallet wrote: >> >> Hi Simon and Cyril, >> >> I really appreciate your insight. >> >> By examining the parameters of the acquisition, I saw that the center >> must effectively be offset (4.8 mm in both directions). For the attached >> image, I also increases sdd and sid by a factor 1000, just in case I would >> be wrong in units. It reduces the first default I pointed out in my first >> message. Also note that my input dataset was SophiaBeads_512_averaged. >> >> Regarding the pre-processing mentioned by Simon, I need more help. Is it >> as simple as the FDK filter assumes that the input is intensity, but the >> dataset provides -ln(I/I0) ? >> >> Regards, >> mg >> >> 2016-01-20 3:33 GMT-05:00 Simon Rit : >> >>> Hi, >>> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >>> is provided is directly the line integral. RTK will process the tif images >>> as if it were a photon count so I converted the tif projections to mha to >>> avoid this. For the conversion, I used another piece of software but you >>> can easily do the same thing with SimpleRTK. >>> Second, I used the enclosed script which gives me a much better result. >>> I have however a geometry problem. I think they provide a Matlab piece of >>> code to get the center of rotation. If you can run it and find out what is >>> this center, then you can use it to configure the geometry better with the >>> options --proj_iso_x and --proj_iso_y. >>> Good luck, >>> Simon >>> >>> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >>> mgvallet.pro at gmail.com> wrote: >>> >>>> Thanks Cyril! >>>> going to carefully check my inputs and I give you some news. >>>> mgv >>>> >>>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>>> cyril.mory at uclouvain.be>: >>>> >>>>> Hi, >>>>> >>>>> It looks like the geometry is wrong indeed, because I have never seen >>>>> such artifacts. >>>>> >>>>> Hope that helps, >>>>> Cyril >>>>> >>>>> >>>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>>> >>>>> Dear rtk-users, >>>>> >>>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>>> https://zenodo.org/record/16539. >>>>> This is a plastic tube filled with glass beads that has been scanned. >>>>> >>>>> Attached is a view of the reconstructed central slice. It is found >>>>> that: >>>>> >>>>> 1. the beads are quickly deformed outside the center >>>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>>> >>>>> My question is if these are simply expected artifacts. I am not 100% >>>>> sure I properly set the geometry parameters. >>>>> >>>>> Regards, >>>>> mgv >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> [image: Avast logo] >>>>> >>>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>>> logiciel antivirus Avast. >>>>> www.avast.com >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Jan 26 17:17:01 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 26 Jan 2016 23:17:01 +0100 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Hi MG, Sometimes, the progressive deformation from the center of rotation to the edge of the image is caused by wrong sdd/sid ratio. Such as change in the geometry will lead to distortion of the image and wrong magnification. Maybe you can play with that parameter and report your result. Cheers, Louie Sent from Mail for Windows 10 From: Simon Rit Sent: Tuesday, January 26, 2016 13:24 To: MG Vallet Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Sophia beads reconstruction Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and?ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was?SophiaBeads_512_averaged. Regarding the pre-processing?mentioned?by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit?: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from?https://zenodo.org/record/16539.? This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts.?I am not 100% sure I properly set the geometry parameters. Regards, mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. www.avast.com _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Thu Jan 28 16:27:15 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 28 Jan 2016 16:27:15 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: Louie, I played with sdd and sid, following your advise. But they have few effect, clearly less effect than proj_iso_x. And none of these parameters can significantly improve my result. Simon, I carefully checked every input data and I cant see what I did wrong. I want first to reproduce your output. You said earlier it's easy to convert a series of tiff image into a mha file using SimpleRTK. Do you mean by writing a short program, or is it possible from the command line ? MG 2016-01-26 17:17 GMT-05:00 louie L : > Hi MG, > > > > Sometimes, the progressive deformation from the center of rotation to the > edge of the image is caused by wrong sdd/sid ratio. Such as change in the > geometry will lead to distortion of the image and wrong magnification. > > Maybe you can play with that parameter and report your result. > > > > Cheers, > > Louie > > > > Sent from Mail for > Windows 10 > > > > > *From: *Simon Rit > *Sent: *Tuesday, January 26, 2016 13:24 > *To: *MG Vallet > *Cc: *rtk-users at public.kitware.com > *Subject: *Re: [Rtk-users] Sophia beads reconstruction > > > > Hi, > > I think it's likely a problem with parameters. The best would be to obtain > them from the Matlab code they provide. > > Good luck, > > Simon > > > > On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > > Hi Simon, > > > > this was a point I missed. I had to do the log mapping. > > > > I must say, I do not use RTK from shell. I just plugged the objects > > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > > > MG > > > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > > > I really appreciate your insight. > > > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > > > Regards, > > mg > > > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > > Hi, > > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > > Good luck, > > Simon > > > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > > Thanks Cyril! > > going to carefully check my inputs and I give you some news. > > mgv > > > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > > This is a plastic tube filled with glass beads that has been scanned. > > > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > > > Regards, > > mgv > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 4 16:55:56 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 4 Jan 2016 16:55:56 -0500 Subject: [Rtk-users] feldkamp application Message-ID: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Tue Jan 5 03:25:50 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 05 Jan 2016 09:25:50 +0100 Subject: [Rtk-users] feldkamp application In-Reply-To: References: Message-ID: <568B7E0E.9030904@uclouvain.be> Hi, and happy new year :) You can use the dataset provided for the motion-compensated reconstruction : http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Hope it helps, Cyril On 01/04/2016 10:55 PM, MG Vallet wrote: > Happy new year! > > Does someone have a data set, other than quadric phantoms, to test the > fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 5 05:16:50 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 5 Jan 2016 11:16:50 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: Message-ID: <568B9812.40404@creatis.insa-lyon.fr> Hi, I forgot to cc this email to the mailing list, in answers to mgv. Simon -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit To: MG Vallet Hi, There are vendor-specific examples available on the wiki: http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction You also have real patient data for 4D CBCT, e.g. http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Simon On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 5 16:50:09 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 5 Jan 2016 16:50:09 -0500 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: <568B9812.40404@creatis.insa-lyon.fr> References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: Thanks, Cyril and Simon. These applications seemed complicated to me, but it's only data reading that is. By the way, the command rtkfieldofview had no effect in the varian case (no error message, nor output file). Otherwise, everything's OK. 2016-01-05 5:16 GMT-05:00 Simon Rit : > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp > application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit > To: MG > Vallet > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet wrote: > >> Happy new year! >> >> Does someone have a data set, other than quadric phantoms, to test the >> fdk module ? >> It would be fine to add one to the wiki page >> http://wiki.openrtk.org/index.php/Main_Page#Applications >> >> mgv >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Mon Jan 11 09:34:58 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Mon, 11 Jan 2016 15:34:58 +0100 Subject: [Rtk-users] Parker weighting In-Reply-To: <56743FCB.3040102@creatis.insa-lyon.fr> References: <56667F38.6040604@creatis.insa-lyon.fr> <56743FCB.3040102@creatis.insa-lyon.fr> Message-ID: Dear Simon, I am sorry for the late reply. I also wish you a happy new year. I will recheck if there is any error during generating projection images. The projections are generated from a volume with our simulation tool. However, I generated projections from the volume with rtkforwardprojections and I re-reconstructed the volume with rtkfdk. I did not get any artifacts. I will contact you soon, if I have some results. Thank you very much for your help. Shiras On Fri, Dec 18, 2015 at 6:18 PM, Simon Rit wrote: > Hi Shiras, > Sorry for the delayed answer, times are busy. The way RTK computes the > spanned arc is from the second projection angle to the before last > projection angle, i.e., in your case > 209.609216488925-11.6067737022482 > so it's a span of 199 degrees and your cone angle is indeed too large. > Like I said, this part of RTK is perfectible and there is no way to change > this but change the code. > However, the source of artefacts might be something else. On simulated > data, I tried: > rtkprojectshepploganphantom --like original_proj.mhd -g > geometry_parker_corr.xml -o proj.mha > rtkfdk -p . -r proj.mha -o fdk.mha -g geometry_parker_corr.xml > and the result is not that bad. What do you think? Can you show us a > snapshot if sg's wrong in your opinion? > Simon > > > On 09/12/2015 11:01, Shiras Abdurahman wrote: > > Dear Simon, > > I am attaching the mhd files of projections. > > With regards, > Shiras > > On Tue, Dec 8, 2015 at 6:17 PM, Simon Rit > wrote: > >> Hi, >> The geometry files look ok to me. What is the projection information? If >> you're still getting the same message as before, I think it's because you >> don't have enough data. If you send the mhd file of the projections (just >> the mhd, not the raw data), I can try to test it on simulated data to let >> you know my feeling. >> Simon >> >> On Tue, Dec 8, 2015 at 5:41 PM, Shiras Abdurahman < >> shiraska at gmail.com> wrote: >> >>> Dear Simon, >>> >>> I tried this option and unfortunately it did not work. I added zero >>> projections and modified geometry files. However, I am getting same >>> artifacts in the volume. Voxel values changed a little bit that indicates >>> during backprojection it still considers extreme projections. I am also >>> getting an output message same as before. >>> >>> I am attaching geometry files. >>> >>> With regards, >>> Shiras >>> >>> On Tue, Dec 8, 2015 at 10:15 AM, Simon Rit < >>> simon.rit at creatis.insa-lyon.fr> wrote: >>> >>>> So calling AddProjection before and after the loop with an adequate >>>> gantry_angle should work. >>>> Simon >>>> >>>> On Tue, Dec 8, 2015 at 9:52 AM, Shiras Abdurahman < >>>> shiraska at gmail.com> wrote: >>>> >>>>> Drear Simon, >>>>> >>>>> I generate the geometry with system geometry parameters and using >>>>> AddProjection method. >>>>> >>>>> Here is the code >>>>> >>>>> >>>>> rtk::ThreeDCircularProjectionGeometry::Pointer rtk_sys_geometry_; >>>>> rtk_sys_geometry_ = rtk::ThreeDCircularProjectionGeometry::New(); >>>>> for (uint16_t proj_index = 0; proj_index < num_projections_; >>>>> proj_index++) >>>>> { >>>>> >>>>> rtk_sys_geometry_->AddProjection(rtk_geom_params_.at(proj_index).sid_mm, >>>>> rtk_geom_params_.at(proj_index).sdd_mm, >>>>> rtk_geom_params_.at(proj_index).gantry_angle_deg, >>>>> rtk_geom_params_.at(proj_index).proj_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).proj_offset_y_mm, >>>>> rtk_geom_params_.at(proj_index).out_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).in_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).src_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).src_offset_y_mm); >>>>> } >>>>> >>>>> And then write to xml file. >>>>> >>>>> Shiras >>>>> >>>>> >>>>> >>>>> On Tue, Dec 8, 2015 at 9:23 AM, Simon Rit < >>>>> simon.rit at creatis.insa-lyon.fr> wrote: >>>>> >>>>>> Hi, >>>>>> rtkfdk.cxx just read the geometry from a file so the best is to >>>>>> modify the geometry file. How do you generate the geometry? >>>>>> For example, if you use rtksimulated geometry, let's say that you >>>>>> were using: >>>>>> rtksimulatedgeometry -n 200 -a 200 -o g.xml >>>>>> then you'll have to replace it with >>>>>> rtksimulatedgeometry -n 202 -a 202 -o g.xml -f -1 >>>>>> Don't forget to add dummy projection at the beginning and the end. If >>>>>> you use a more complex geometry, maybe SimpleRTK >>>>>> can be helpful >>>>>> (I'd use that) or you'd have to modify the cxx code to add these additional >>>>>> projections in the geometry and the projection stack. >>>>>> Simon >>>>>> >>>>>> >>>>>> On Tue, Dec 8, 2015 at 8:51 AM, Shiras Abdurahman < >>>>>> shiraska at gmail.com> wrote: >>>>>> >>>>>>> Dear Simon, >>>>>>> >>>>>>> Thanks a lot for the reply. Can you please inform me how can I set >>>>>>> where the arc starts? >>>>>>> Do I need to modify geometry also? >>>>>>> If you can point the line of code rtkfdk.cxx, it will be really >>>>>>> helpful. >>>>>>> >>>>>>> With regards, >>>>>>> Shiras >>>>>>> >>>>>>> On Tue, Dec 8, 2015 at 7:56 AM, Simon Rit < >>>>>>> simon.rit at creatis.insa-lyon.fr> >>>>>>> wrote: >>>>>>> >>>>>>>> Dear Shiras, >>>>>>>> Yes, for practical reasons the first and the last projections are >>>>>>>> set to 0 and the arc used in the Parker weighting starts between the first >>>>>>>> two projections and ends between the lasts two projections. There is a >>>>>>>> simple solution: add a projection at the beginning and the end of the arc, >>>>>>>> which can contain any pixel values but should be set where you want this >>>>>>>> arc to start. In the future, I think someone should once take the time to >>>>>>>> correct this but I haven't so far. I'll keep you posted on the mailing list >>>>>>>> when it's corrected. >>>>>>>> Simon >>>>>>>> >>>>>>>> On 07/12/2015 12:04, Shiras Abdurahman wrote: >>>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I am trying to reconstruct a volume from projection data generated >>>>>>>> with C-arm CT. There are 248 projections with an angular range of 199 >>>>>>>> degree. Technically, parker weighting should run without any problems. >>>>>>>> However, I am getting an output message that "You do not have enough data >>>>>>>> for proper parker weighting". After parker weighting, the two extreme >>>>>>>> projections (projection number 1 and 248) were completely zero and thus >>>>>>>> reconstructed volume contained artifacts. When I increased the angular >>>>>>>> range, this problem did not happen. How can I solve this problem without >>>>>>>> increasing angular range? Is there any threshold constant that I can change >>>>>>>> in command line or in my code? >>>>>>>> >>>>>>>> I really appreciate any help you can provide. >>>>>>>> >>>>>>>> With regards, >>>>>>>> Shiras >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 12 07:47:46 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 12 Jan 2016 13:47:46 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: <5694F5F2.4060702@creatis.insa-lyon.fr> Hi, There was a typo on the folder path (../Scan0 instead of Scan0). Was that the problem? I checked and it has the expected effect, i.e., setting to 0 everything outside the FOV. Simon On 05/01/2016 22:50, MG Vallet wrote: > Thanks, Cyril and Simon. > These applications seemed complicated to me, but it's only data > reading that is. > By the way, the command rtkfieldofview had no effect in the varian > case (no error message, nor output file). Otherwise, everything's OK. > > 2016-01-05 5:16 GMT-05:00 Simon Rit >: > > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- > Subject: Re: [Rtk-users] feldkamp application > Date: Tue, 5 Jan 2016 08:40:00 +0100 > From: Simon Rit > > To: MG Vallet > > > > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: > > Happy new year! > > Does someone have a data set, other than quadric phantoms, to > test the fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Wed Jan 13 07:42:45 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Wed, 13 Jan 2016 13:42:45 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry Message-ID: Dear all, I am trying to generate geometry xml file with rtkReg23ProjectionGeometry after decomposing projection matrix. One of the argument to the function AddReg23Projection is detector position. I assume that, it is the position vector of the center of the first pixel in world co-ordinates. This will be used for computing the projection offset parameters by projecting detector origin vector onto the u and v axis of the detector. If that is the case, do we need to change the offset parameters of each projection in the mhd file. Will this create problems during displaced detector correction? With regards, Shiras -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 13 13:31:23 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Jan 2016 19:31:23 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry In-Reply-To: References: Message-ID: <569697FB.1020804@creatis.insa-lyon.fr> Hi, Wrong assumption. It's the coordinate of point (0,0) in the coordinate of the projection image in the word coordinates, it's not the coordinate of the center of the first pixel. This is mentioned in the geometry description file on the wiki. You should not change the mhd parameters. If you want to account for offset parameters that change from projection to projection, you can put that offset in the computation of the detector position in world coordinates. Simon On 13/01/2016 13:42, Shiras Abdurahman wrote: > Dear all, > > I am trying to generate geometry xml file with > rtkReg23ProjectionGeometry after decomposing projection matrix. One of > the argument to the function AddReg23Projection is detector position. > I assume that, it is the position vector of the center of the first > pixel in world co-ordinates. This will be used for computing the > projection offset parameters by projecting detector origin vector onto > the u and v axis of the detector. If that is the case, do we need to > change the offset parameters of each projection in the mhd file. Will > this create problems during displaced detector correction? > > > With regards, > Shiras > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 10:19:12 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 10:19:12 -0500 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from https://zenodo.org/record/16539. This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts. I am not 100% sure I properly set the geometry parameters. Regards, mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sophiaBeadsCentralSlide.jpg Type: image/jpeg Size: 55394 bytes Desc: not available URL: From cyril.mory at uclouvain.be Tue Jan 19 10:33:02 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 19 Jan 2016 16:33:02 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: <569E572E.20203@uclouvain.be> Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit : > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% > sure I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users --- L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 14:02:45 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 14:02:45 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <569E572E.20203@uclouvain.be> References: <569E572E.20203@uclouvain.be> Message-ID: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > > ------------------------------ > [image: Avast logo] > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 20 03:33:47 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 20 Jan 2016 09:33:47 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > >> Hi, >> >> It looks like the geometry is wrong indeed, because I have never seen >> such artifacts. >> >> Hope that helps, >> Cyril >> >> >> Le 19/01/2016 16:19, MG Vallet a ?crit : >> >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data set from >> https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has been scanned. >> >> Attached is a view of the reconstructed central slice. It is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the proper term) >> >> My question is if these are simply expected artifacts. I am not 100% >> sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> >> ------------------------------ >> [image: Avast logo] >> >> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >> logiciel antivirus Avast. >> www.avast.com >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkfdk.sh Type: application/x-sh Size: 404 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: snapshot.jpg Type: image/jpeg Size: 95222 bytes Desc: not available URL: From mgvallet.pro at gmail.com Thu Jan 21 14:02:28 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 21 Jan 2016 14:02:28 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was SophiaBeads_512_averaged. Regarding the pre-processing mentioned by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > >> Thanks Cyril! >> going to carefully check my inputs and I give you some news. >> mgv >> >> 2016-01-19 10:33 GMT-05:00 Cyril Mory : >> >>> Hi, >>> >>> It looks like the geometry is wrong indeed, because I have never seen >>> such artifacts. >>> >>> Hope that helps, >>> Cyril >>> >>> >>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>> >>> Dear rtk-users, >>> >>> I applied the FDKConeBeamReconstructionFilter to a data set from >>> https://zenodo.org/record/16539. >>> This is a plastic tube filled with glass beads that has been scanned. >>> >>> Attached is a view of the reconstructed central slice. It is found that: >>> >>> 1. the beads are quickly deformed outside the center >>> 2. each one has a halo, or a shadow (dont know the proper term) >>> >>> My question is if these are simply expected artifacts. I am not 100% >>> sure I properly set the geometry parameters. >>> >>> Regards, >>> mgv >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >>> >>> ------------------------------ >>> [image: Avast logo] >>> >>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>> logiciel antivirus Avast. >>> www.avast.com >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_offset.jpg Type: image/jpeg Size: 52844 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Thu Jan 21 14:22:55 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Jan 2016 20:22:55 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: <56A1300F.1090509@creatis.insa-lyon.fr> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center > must effectively be offset (4.8 mm in both directions). For the > attached image, I also increases sdd and sid by a factor 1000, just in > case I would be wrong in units. It reduces the first default I pointed > out in my first message. Also note that my input dataset was > SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is > it as simple as the FDK filter assumes that the input is intensity, > but the dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit >: > > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems > that what is provided is directly the line integral. RTK will > process the tif images as if it were a photon count so I converted > the tif projections to mha to avoid this. For the conversion, I > used another piece of software but you can easily do the same > thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better > result. I have however a geometry problem. I think they provide a > Matlab piece of code to get the center of rotation. If you can run > it and find out what is this center, then you can use it to > configure the geometry better with the options --proj_iso_x and > --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet > wrote: > > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory >: > > Hi, > > It looks like the geometry is wrong indeed, because I have > never seen such artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data >> set from https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has >> been scanned. >> >> Attached is a view of the reconstructed central slice. It >> is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the >> proper term) >> >> My question is if these are simply expected artifacts. I >> am not 100% sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> >> http://public.kitware.com/mailman/listinfo/rtk-users > > > > ------------------------------------------------------------------------ > Avast logo > > L'absence de virus dans ce courrier ?lectronique a ?t? > v?rifi?e par le logiciel antivirus Avast. > www.avast.com > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 25 11:48:35 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 25 Jan 2016 11:48:35 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <56A1300F.1090509@creatis.insa-lyon.fr> References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > >> Hi, >> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >> is provided is directly the line integral. RTK will process the tif images >> as if it were a photon count so I converted the tif projections to mha to >> avoid this. For the conversion, I used another piece of software but you >> can easily do the same thing with SimpleRTK. >> Second, I used the enclosed script which gives me a much better result. I >> have however a geometry problem. I think they provide a Matlab piece of >> code to get the center of rotation. If you can run it and find out what is >> this center, then you can use it to configure the geometry better with the >> options --proj_iso_x and --proj_iso_y. >> Good luck, >> Simon >> >> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >> mgvallet.pro at gmail.com> wrote: >> >>> Thanks Cyril! >>> going to carefully check my inputs and I give you some news. >>> mgv >>> >>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>> cyril.mory at uclouvain.be>: >>> >>>> Hi, >>>> >>>> It looks like the geometry is wrong indeed, because I have never seen >>>> such artifacts. >>>> >>>> Hope that helps, >>>> Cyril >>>> >>>> >>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>> >>>> Dear rtk-users, >>>> >>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>> https://zenodo.org/record/16539. >>>> This is a plastic tube filled with glass beads that has been scanned. >>>> >>>> Attached is a view of the reconstructed central slice. It is found that: >>>> >>>> 1. the beads are quickly deformed outside the center >>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>> >>>> My question is if these are simply expected artifacts. I am not 100% >>>> sure I properly set the geometry parameters. >>>> >>>> Regards, >>>> mgv >>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> [image: Avast logo] >>>> >>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>> logiciel antivirus Avast. >>>> www.avast.com >>>> >>>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_log.jpg Type: image/jpeg Size: 17331 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 26 07:23:58 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Jan 2016 13:23:58 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > Hi Simon, > > this was a point I missed. I had to do the log mapping. > > I must say, I do not use RTK from shell. I just plugged the objects > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > MG > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > >> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the >> line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the >> projections and converts them depending on the type: for mha or mhd, it >> just reads it and nothing else. For tif, it assumes that I is passed, try >> to guess I0 (or gets it from the cmd line) and computes ln(I0/I). >> So from each tif projection, instead of letting them go through the >> ProjectionsReader in RTK, directly use the ImageReader, stack them and pass >> it to the reconstruction algorithm. In other words, if you use SimpleRTK, >> use ImageSeriesReader instead of ProjectionsReader. >> Regarding the geometry, it would be nice to be confident in the geometry >> parameters, maybe from their Matlab code? >> Simon >> >> >> On 21/01/2016 20:02, MG Vallet wrote: >> >> Hi Simon and Cyril, >> >> I really appreciate your insight. >> >> By examining the parameters of the acquisition, I saw that the center >> must effectively be offset (4.8 mm in both directions). For the attached >> image, I also increases sdd and sid by a factor 1000, just in case I would >> be wrong in units. It reduces the first default I pointed out in my first >> message. Also note that my input dataset was SophiaBeads_512_averaged. >> >> Regarding the pre-processing mentioned by Simon, I need more help. Is it >> as simple as the FDK filter assumes that the input is intensity, but the >> dataset provides -ln(I/I0) ? >> >> Regards, >> mg >> >> 2016-01-20 3:33 GMT-05:00 Simon Rit : >> >>> Hi, >>> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >>> is provided is directly the line integral. RTK will process the tif images >>> as if it were a photon count so I converted the tif projections to mha to >>> avoid this. For the conversion, I used another piece of software but you >>> can easily do the same thing with SimpleRTK. >>> Second, I used the enclosed script which gives me a much better result. >>> I have however a geometry problem. I think they provide a Matlab piece of >>> code to get the center of rotation. If you can run it and find out what is >>> this center, then you can use it to configure the geometry better with the >>> options --proj_iso_x and --proj_iso_y. >>> Good luck, >>> Simon >>> >>> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >>> mgvallet.pro at gmail.com> wrote: >>> >>>> Thanks Cyril! >>>> going to carefully check my inputs and I give you some news. >>>> mgv >>>> >>>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>>> cyril.mory at uclouvain.be>: >>>> >>>>> Hi, >>>>> >>>>> It looks like the geometry is wrong indeed, because I have never seen >>>>> such artifacts. >>>>> >>>>> Hope that helps, >>>>> Cyril >>>>> >>>>> >>>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>>> >>>>> Dear rtk-users, >>>>> >>>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>>> https://zenodo.org/record/16539. >>>>> This is a plastic tube filled with glass beads that has been scanned. >>>>> >>>>> Attached is a view of the reconstructed central slice. It is found >>>>> that: >>>>> >>>>> 1. the beads are quickly deformed outside the center >>>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>>> >>>>> My question is if these are simply expected artifacts. I am not 100% >>>>> sure I properly set the geometry parameters. >>>>> >>>>> Regards, >>>>> mgv >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> [image: Avast logo] >>>>> >>>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>>> logiciel antivirus Avast. >>>>> www.avast.com >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Jan 26 17:17:01 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 26 Jan 2016 23:17:01 +0100 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Hi MG, Sometimes, the progressive deformation from the center of rotation to the edge of the image is caused by wrong sdd/sid ratio. Such as change in the geometry will lead to distortion of the image and wrong magnification. Maybe you can play with that parameter and report your result. Cheers, Louie Sent from Mail for Windows 10 From: Simon Rit Sent: Tuesday, January 26, 2016 13:24 To: MG Vallet Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Sophia beads reconstruction Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and?ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was?SophiaBeads_512_averaged. Regarding the pre-processing?mentioned?by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit?: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from?https://zenodo.org/record/16539.? This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts.?I am not 100% sure I properly set the geometry parameters. Regards, mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. www.avast.com _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Thu Jan 28 16:27:15 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 28 Jan 2016 16:27:15 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: Louie, I played with sdd and sid, following your advise. But they have few effect, clearly less effect than proj_iso_x. And none of these parameters can significantly improve my result. Simon, I carefully checked every input data and I cant see what I did wrong. I want first to reproduce your output. You said earlier it's easy to convert a series of tiff image into a mha file using SimpleRTK. Do you mean by writing a short program, or is it possible from the command line ? MG 2016-01-26 17:17 GMT-05:00 louie L : > Hi MG, > > > > Sometimes, the progressive deformation from the center of rotation to the > edge of the image is caused by wrong sdd/sid ratio. Such as change in the > geometry will lead to distortion of the image and wrong magnification. > > Maybe you can play with that parameter and report your result. > > > > Cheers, > > Louie > > > > Sent from Mail for > Windows 10 > > > > > *From: *Simon Rit > *Sent: *Tuesday, January 26, 2016 13:24 > *To: *MG Vallet > *Cc: *rtk-users at public.kitware.com > *Subject: *Re: [Rtk-users] Sophia beads reconstruction > > > > Hi, > > I think it's likely a problem with parameters. The best would be to obtain > them from the Matlab code they provide. > > Good luck, > > Simon > > > > On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > > Hi Simon, > > > > this was a point I missed. I had to do the log mapping. > > > > I must say, I do not use RTK from shell. I just plugged the objects > > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > > > MG > > > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > > > I really appreciate your insight. > > > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > > > Regards, > > mg > > > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > > Hi, > > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > > Good luck, > > Simon > > > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > > Thanks Cyril! > > going to carefully check my inputs and I give you some news. > > mgv > > > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > > This is a plastic tube filled with glass beads that has been scanned. > > > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > > > Regards, > > mgv > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 4 16:55:56 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 4 Jan 2016 16:55:56 -0500 Subject: [Rtk-users] feldkamp application Message-ID: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Tue Jan 5 03:25:50 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 05 Jan 2016 09:25:50 +0100 Subject: [Rtk-users] feldkamp application In-Reply-To: References: Message-ID: <568B7E0E.9030904@uclouvain.be> Hi, and happy new year :) You can use the dataset provided for the motion-compensated reconstruction : http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Hope it helps, Cyril On 01/04/2016 10:55 PM, MG Vallet wrote: > Happy new year! > > Does someone have a data set, other than quadric phantoms, to test the > fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 5 05:16:50 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 5 Jan 2016 11:16:50 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: Message-ID: <568B9812.40404@creatis.insa-lyon.fr> Hi, I forgot to cc this email to the mailing list, in answers to mgv. Simon -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit To: MG Vallet Hi, There are vendor-specific examples available on the wiki: http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction You also have real patient data for 4D CBCT, e.g. http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Simon On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 5 16:50:09 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 5 Jan 2016 16:50:09 -0500 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: <568B9812.40404@creatis.insa-lyon.fr> References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: Thanks, Cyril and Simon. These applications seemed complicated to me, but it's only data reading that is. By the way, the command rtkfieldofview had no effect in the varian case (no error message, nor output file). Otherwise, everything's OK. 2016-01-05 5:16 GMT-05:00 Simon Rit : > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp > application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit > To: MG > Vallet > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet wrote: > >> Happy new year! >> >> Does someone have a data set, other than quadric phantoms, to test the >> fdk module ? >> It would be fine to add one to the wiki page >> http://wiki.openrtk.org/index.php/Main_Page#Applications >> >> mgv >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Mon Jan 11 09:34:58 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Mon, 11 Jan 2016 15:34:58 +0100 Subject: [Rtk-users] Parker weighting In-Reply-To: <56743FCB.3040102@creatis.insa-lyon.fr> References: <56667F38.6040604@creatis.insa-lyon.fr> <56743FCB.3040102@creatis.insa-lyon.fr> Message-ID: Dear Simon, I am sorry for the late reply. I also wish you a happy new year. I will recheck if there is any error during generating projection images. The projections are generated from a volume with our simulation tool. However, I generated projections from the volume with rtkforwardprojections and I re-reconstructed the volume with rtkfdk. I did not get any artifacts. I will contact you soon, if I have some results. Thank you very much for your help. Shiras On Fri, Dec 18, 2015 at 6:18 PM, Simon Rit wrote: > Hi Shiras, > Sorry for the delayed answer, times are busy. The way RTK computes the > spanned arc is from the second projection angle to the before last > projection angle, i.e., in your case > 209.609216488925-11.6067737022482 > so it's a span of 199 degrees and your cone angle is indeed too large. > Like I said, this part of RTK is perfectible and there is no way to change > this but change the code. > However, the source of artefacts might be something else. On simulated > data, I tried: > rtkprojectshepploganphantom --like original_proj.mhd -g > geometry_parker_corr.xml -o proj.mha > rtkfdk -p . -r proj.mha -o fdk.mha -g geometry_parker_corr.xml > and the result is not that bad. What do you think? Can you show us a > snapshot if sg's wrong in your opinion? > Simon > > > On 09/12/2015 11:01, Shiras Abdurahman wrote: > > Dear Simon, > > I am attaching the mhd files of projections. > > With regards, > Shiras > > On Tue, Dec 8, 2015 at 6:17 PM, Simon Rit > wrote: > >> Hi, >> The geometry files look ok to me. What is the projection information? If >> you're still getting the same message as before, I think it's because you >> don't have enough data. If you send the mhd file of the projections (just >> the mhd, not the raw data), I can try to test it on simulated data to let >> you know my feeling. >> Simon >> >> On Tue, Dec 8, 2015 at 5:41 PM, Shiras Abdurahman < >> shiraska at gmail.com> wrote: >> >>> Dear Simon, >>> >>> I tried this option and unfortunately it did not work. I added zero >>> projections and modified geometry files. However, I am getting same >>> artifacts in the volume. Voxel values changed a little bit that indicates >>> during backprojection it still considers extreme projections. I am also >>> getting an output message same as before. >>> >>> I am attaching geometry files. >>> >>> With regards, >>> Shiras >>> >>> On Tue, Dec 8, 2015 at 10:15 AM, Simon Rit < >>> simon.rit at creatis.insa-lyon.fr> wrote: >>> >>>> So calling AddProjection before and after the loop with an adequate >>>> gantry_angle should work. >>>> Simon >>>> >>>> On Tue, Dec 8, 2015 at 9:52 AM, Shiras Abdurahman < >>>> shiraska at gmail.com> wrote: >>>> >>>>> Drear Simon, >>>>> >>>>> I generate the geometry with system geometry parameters and using >>>>> AddProjection method. >>>>> >>>>> Here is the code >>>>> >>>>> >>>>> rtk::ThreeDCircularProjectionGeometry::Pointer rtk_sys_geometry_; >>>>> rtk_sys_geometry_ = rtk::ThreeDCircularProjectionGeometry::New(); >>>>> for (uint16_t proj_index = 0; proj_index < num_projections_; >>>>> proj_index++) >>>>> { >>>>> >>>>> rtk_sys_geometry_->AddProjection(rtk_geom_params_.at(proj_index).sid_mm, >>>>> rtk_geom_params_.at(proj_index).sdd_mm, >>>>> rtk_geom_params_.at(proj_index).gantry_angle_deg, >>>>> rtk_geom_params_.at(proj_index).proj_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).proj_offset_y_mm, >>>>> rtk_geom_params_.at(proj_index).out_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).in_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).src_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).src_offset_y_mm); >>>>> } >>>>> >>>>> And then write to xml file. >>>>> >>>>> Shiras >>>>> >>>>> >>>>> >>>>> On Tue, Dec 8, 2015 at 9:23 AM, Simon Rit < >>>>> simon.rit at creatis.insa-lyon.fr> wrote: >>>>> >>>>>> Hi, >>>>>> rtkfdk.cxx just read the geometry from a file so the best is to >>>>>> modify the geometry file. How do you generate the geometry? >>>>>> For example, if you use rtksimulated geometry, let's say that you >>>>>> were using: >>>>>> rtksimulatedgeometry -n 200 -a 200 -o g.xml >>>>>> then you'll have to replace it with >>>>>> rtksimulatedgeometry -n 202 -a 202 -o g.xml -f -1 >>>>>> Don't forget to add dummy projection at the beginning and the end. If >>>>>> you use a more complex geometry, maybe SimpleRTK >>>>>> can be helpful >>>>>> (I'd use that) or you'd have to modify the cxx code to add these additional >>>>>> projections in the geometry and the projection stack. >>>>>> Simon >>>>>> >>>>>> >>>>>> On Tue, Dec 8, 2015 at 8:51 AM, Shiras Abdurahman < >>>>>> shiraska at gmail.com> wrote: >>>>>> >>>>>>> Dear Simon, >>>>>>> >>>>>>> Thanks a lot for the reply. Can you please inform me how can I set >>>>>>> where the arc starts? >>>>>>> Do I need to modify geometry also? >>>>>>> If you can point the line of code rtkfdk.cxx, it will be really >>>>>>> helpful. >>>>>>> >>>>>>> With regards, >>>>>>> Shiras >>>>>>> >>>>>>> On Tue, Dec 8, 2015 at 7:56 AM, Simon Rit < >>>>>>> simon.rit at creatis.insa-lyon.fr> >>>>>>> wrote: >>>>>>> >>>>>>>> Dear Shiras, >>>>>>>> Yes, for practical reasons the first and the last projections are >>>>>>>> set to 0 and the arc used in the Parker weighting starts between the first >>>>>>>> two projections and ends between the lasts two projections. There is a >>>>>>>> simple solution: add a projection at the beginning and the end of the arc, >>>>>>>> which can contain any pixel values but should be set where you want this >>>>>>>> arc to start. In the future, I think someone should once take the time to >>>>>>>> correct this but I haven't so far. I'll keep you posted on the mailing list >>>>>>>> when it's corrected. >>>>>>>> Simon >>>>>>>> >>>>>>>> On 07/12/2015 12:04, Shiras Abdurahman wrote: >>>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I am trying to reconstruct a volume from projection data generated >>>>>>>> with C-arm CT. There are 248 projections with an angular range of 199 >>>>>>>> degree. Technically, parker weighting should run without any problems. >>>>>>>> However, I am getting an output message that "You do not have enough data >>>>>>>> for proper parker weighting". After parker weighting, the two extreme >>>>>>>> projections (projection number 1 and 248) were completely zero and thus >>>>>>>> reconstructed volume contained artifacts. When I increased the angular >>>>>>>> range, this problem did not happen. How can I solve this problem without >>>>>>>> increasing angular range? Is there any threshold constant that I can change >>>>>>>> in command line or in my code? >>>>>>>> >>>>>>>> I really appreciate any help you can provide. >>>>>>>> >>>>>>>> With regards, >>>>>>>> Shiras >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 12 07:47:46 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 12 Jan 2016 13:47:46 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: <5694F5F2.4060702@creatis.insa-lyon.fr> Hi, There was a typo on the folder path (../Scan0 instead of Scan0). Was that the problem? I checked and it has the expected effect, i.e., setting to 0 everything outside the FOV. Simon On 05/01/2016 22:50, MG Vallet wrote: > Thanks, Cyril and Simon. > These applications seemed complicated to me, but it's only data > reading that is. > By the way, the command rtkfieldofview had no effect in the varian > case (no error message, nor output file). Otherwise, everything's OK. > > 2016-01-05 5:16 GMT-05:00 Simon Rit >: > > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- > Subject: Re: [Rtk-users] feldkamp application > Date: Tue, 5 Jan 2016 08:40:00 +0100 > From: Simon Rit > > To: MG Vallet > > > > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: > > Happy new year! > > Does someone have a data set, other than quadric phantoms, to > test the fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Wed Jan 13 07:42:45 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Wed, 13 Jan 2016 13:42:45 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry Message-ID: Dear all, I am trying to generate geometry xml file with rtkReg23ProjectionGeometry after decomposing projection matrix. One of the argument to the function AddReg23Projection is detector position. I assume that, it is the position vector of the center of the first pixel in world co-ordinates. This will be used for computing the projection offset parameters by projecting detector origin vector onto the u and v axis of the detector. If that is the case, do we need to change the offset parameters of each projection in the mhd file. Will this create problems during displaced detector correction? With regards, Shiras -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 13 13:31:23 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Jan 2016 19:31:23 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry In-Reply-To: References: Message-ID: <569697FB.1020804@creatis.insa-lyon.fr> Hi, Wrong assumption. It's the coordinate of point (0,0) in the coordinate of the projection image in the word coordinates, it's not the coordinate of the center of the first pixel. This is mentioned in the geometry description file on the wiki. You should not change the mhd parameters. If you want to account for offset parameters that change from projection to projection, you can put that offset in the computation of the detector position in world coordinates. Simon On 13/01/2016 13:42, Shiras Abdurahman wrote: > Dear all, > > I am trying to generate geometry xml file with > rtkReg23ProjectionGeometry after decomposing projection matrix. One of > the argument to the function AddReg23Projection is detector position. > I assume that, it is the position vector of the center of the first > pixel in world co-ordinates. This will be used for computing the > projection offset parameters by projecting detector origin vector onto > the u and v axis of the detector. If that is the case, do we need to > change the offset parameters of each projection in the mhd file. Will > this create problems during displaced detector correction? > > > With regards, > Shiras > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 10:19:12 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 10:19:12 -0500 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from https://zenodo.org/record/16539. This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts. I am not 100% sure I properly set the geometry parameters. Regards, mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sophiaBeadsCentralSlide.jpg Type: image/jpeg Size: 55394 bytes Desc: not available URL: From cyril.mory at uclouvain.be Tue Jan 19 10:33:02 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 19 Jan 2016 16:33:02 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: <569E572E.20203@uclouvain.be> Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit : > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% > sure I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users --- L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 14:02:45 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 14:02:45 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <569E572E.20203@uclouvain.be> References: <569E572E.20203@uclouvain.be> Message-ID: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > > ------------------------------ > [image: Avast logo] > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 20 03:33:47 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 20 Jan 2016 09:33:47 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > >> Hi, >> >> It looks like the geometry is wrong indeed, because I have never seen >> such artifacts. >> >> Hope that helps, >> Cyril >> >> >> Le 19/01/2016 16:19, MG Vallet a ?crit : >> >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data set from >> https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has been scanned. >> >> Attached is a view of the reconstructed central slice. It is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the proper term) >> >> My question is if these are simply expected artifacts. I am not 100% >> sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> >> ------------------------------ >> [image: Avast logo] >> >> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >> logiciel antivirus Avast. >> www.avast.com >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkfdk.sh Type: application/x-sh Size: 404 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: snapshot.jpg Type: image/jpeg Size: 95222 bytes Desc: not available URL: From mgvallet.pro at gmail.com Thu Jan 21 14:02:28 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 21 Jan 2016 14:02:28 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was SophiaBeads_512_averaged. Regarding the pre-processing mentioned by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > >> Thanks Cyril! >> going to carefully check my inputs and I give you some news. >> mgv >> >> 2016-01-19 10:33 GMT-05:00 Cyril Mory : >> >>> Hi, >>> >>> It looks like the geometry is wrong indeed, because I have never seen >>> such artifacts. >>> >>> Hope that helps, >>> Cyril >>> >>> >>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>> >>> Dear rtk-users, >>> >>> I applied the FDKConeBeamReconstructionFilter to a data set from >>> https://zenodo.org/record/16539. >>> This is a plastic tube filled with glass beads that has been scanned. >>> >>> Attached is a view of the reconstructed central slice. It is found that: >>> >>> 1. the beads are quickly deformed outside the center >>> 2. each one has a halo, or a shadow (dont know the proper term) >>> >>> My question is if these are simply expected artifacts. I am not 100% >>> sure I properly set the geometry parameters. >>> >>> Regards, >>> mgv >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >>> >>> ------------------------------ >>> [image: Avast logo] >>> >>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>> logiciel antivirus Avast. >>> www.avast.com >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_offset.jpg Type: image/jpeg Size: 52844 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Thu Jan 21 14:22:55 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Jan 2016 20:22:55 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: <56A1300F.1090509@creatis.insa-lyon.fr> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center > must effectively be offset (4.8 mm in both directions). For the > attached image, I also increases sdd and sid by a factor 1000, just in > case I would be wrong in units. It reduces the first default I pointed > out in my first message. Also note that my input dataset was > SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is > it as simple as the FDK filter assumes that the input is intensity, > but the dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit >: > > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems > that what is provided is directly the line integral. RTK will > process the tif images as if it were a photon count so I converted > the tif projections to mha to avoid this. For the conversion, I > used another piece of software but you can easily do the same > thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better > result. I have however a geometry problem. I think they provide a > Matlab piece of code to get the center of rotation. If you can run > it and find out what is this center, then you can use it to > configure the geometry better with the options --proj_iso_x and > --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet > wrote: > > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory >: > > Hi, > > It looks like the geometry is wrong indeed, because I have > never seen such artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data >> set from https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has >> been scanned. >> >> Attached is a view of the reconstructed central slice. It >> is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the >> proper term) >> >> My question is if these are simply expected artifacts. I >> am not 100% sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> >> http://public.kitware.com/mailman/listinfo/rtk-users > > > > ------------------------------------------------------------------------ > Avast logo > > L'absence de virus dans ce courrier ?lectronique a ?t? > v?rifi?e par le logiciel antivirus Avast. > www.avast.com > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 25 11:48:35 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 25 Jan 2016 11:48:35 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <56A1300F.1090509@creatis.insa-lyon.fr> References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > >> Hi, >> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >> is provided is directly the line integral. RTK will process the tif images >> as if it were a photon count so I converted the tif projections to mha to >> avoid this. For the conversion, I used another piece of software but you >> can easily do the same thing with SimpleRTK. >> Second, I used the enclosed script which gives me a much better result. I >> have however a geometry problem. I think they provide a Matlab piece of >> code to get the center of rotation. If you can run it and find out what is >> this center, then you can use it to configure the geometry better with the >> options --proj_iso_x and --proj_iso_y. >> Good luck, >> Simon >> >> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >> mgvallet.pro at gmail.com> wrote: >> >>> Thanks Cyril! >>> going to carefully check my inputs and I give you some news. >>> mgv >>> >>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>> cyril.mory at uclouvain.be>: >>> >>>> Hi, >>>> >>>> It looks like the geometry is wrong indeed, because I have never seen >>>> such artifacts. >>>> >>>> Hope that helps, >>>> Cyril >>>> >>>> >>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>> >>>> Dear rtk-users, >>>> >>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>> https://zenodo.org/record/16539. >>>> This is a plastic tube filled with glass beads that has been scanned. >>>> >>>> Attached is a view of the reconstructed central slice. It is found that: >>>> >>>> 1. the beads are quickly deformed outside the center >>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>> >>>> My question is if these are simply expected artifacts. I am not 100% >>>> sure I properly set the geometry parameters. >>>> >>>> Regards, >>>> mgv >>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> [image: Avast logo] >>>> >>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>> logiciel antivirus Avast. >>>> www.avast.com >>>> >>>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_log.jpg Type: image/jpeg Size: 17331 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 26 07:23:58 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Jan 2016 13:23:58 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > Hi Simon, > > this was a point I missed. I had to do the log mapping. > > I must say, I do not use RTK from shell. I just plugged the objects > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > MG > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > >> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the >> line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the >> projections and converts them depending on the type: for mha or mhd, it >> just reads it and nothing else. For tif, it assumes that I is passed, try >> to guess I0 (or gets it from the cmd line) and computes ln(I0/I). >> So from each tif projection, instead of letting them go through the >> ProjectionsReader in RTK, directly use the ImageReader, stack them and pass >> it to the reconstruction algorithm. In other words, if you use SimpleRTK, >> use ImageSeriesReader instead of ProjectionsReader. >> Regarding the geometry, it would be nice to be confident in the geometry >> parameters, maybe from their Matlab code? >> Simon >> >> >> On 21/01/2016 20:02, MG Vallet wrote: >> >> Hi Simon and Cyril, >> >> I really appreciate your insight. >> >> By examining the parameters of the acquisition, I saw that the center >> must effectively be offset (4.8 mm in both directions). For the attached >> image, I also increases sdd and sid by a factor 1000, just in case I would >> be wrong in units. It reduces the first default I pointed out in my first >> message. Also note that my input dataset was SophiaBeads_512_averaged. >> >> Regarding the pre-processing mentioned by Simon, I need more help. Is it >> as simple as the FDK filter assumes that the input is intensity, but the >> dataset provides -ln(I/I0) ? >> >> Regards, >> mg >> >> 2016-01-20 3:33 GMT-05:00 Simon Rit : >> >>> Hi, >>> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >>> is provided is directly the line integral. RTK will process the tif images >>> as if it were a photon count so I converted the tif projections to mha to >>> avoid this. For the conversion, I used another piece of software but you >>> can easily do the same thing with SimpleRTK. >>> Second, I used the enclosed script which gives me a much better result. >>> I have however a geometry problem. I think they provide a Matlab piece of >>> code to get the center of rotation. If you can run it and find out what is >>> this center, then you can use it to configure the geometry better with the >>> options --proj_iso_x and --proj_iso_y. >>> Good luck, >>> Simon >>> >>> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >>> mgvallet.pro at gmail.com> wrote: >>> >>>> Thanks Cyril! >>>> going to carefully check my inputs and I give you some news. >>>> mgv >>>> >>>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>>> cyril.mory at uclouvain.be>: >>>> >>>>> Hi, >>>>> >>>>> It looks like the geometry is wrong indeed, because I have never seen >>>>> such artifacts. >>>>> >>>>> Hope that helps, >>>>> Cyril >>>>> >>>>> >>>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>>> >>>>> Dear rtk-users, >>>>> >>>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>>> https://zenodo.org/record/16539. >>>>> This is a plastic tube filled with glass beads that has been scanned. >>>>> >>>>> Attached is a view of the reconstructed central slice. It is found >>>>> that: >>>>> >>>>> 1. the beads are quickly deformed outside the center >>>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>>> >>>>> My question is if these are simply expected artifacts. I am not 100% >>>>> sure I properly set the geometry parameters. >>>>> >>>>> Regards, >>>>> mgv >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> [image: Avast logo] >>>>> >>>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>>> logiciel antivirus Avast. >>>>> www.avast.com >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Jan 26 17:17:01 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 26 Jan 2016 23:17:01 +0100 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Hi MG, Sometimes, the progressive deformation from the center of rotation to the edge of the image is caused by wrong sdd/sid ratio. Such as change in the geometry will lead to distortion of the image and wrong magnification. Maybe you can play with that parameter and report your result. Cheers, Louie Sent from Mail for Windows 10 From: Simon Rit Sent: Tuesday, January 26, 2016 13:24 To: MG Vallet Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Sophia beads reconstruction Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and?ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was?SophiaBeads_512_averaged. Regarding the pre-processing?mentioned?by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit?: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from?https://zenodo.org/record/16539.? This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts.?I am not 100% sure I properly set the geometry parameters. Regards, mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. www.avast.com _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Thu Jan 28 16:27:15 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 28 Jan 2016 16:27:15 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: Louie, I played with sdd and sid, following your advise. But they have few effect, clearly less effect than proj_iso_x. And none of these parameters can significantly improve my result. Simon, I carefully checked every input data and I cant see what I did wrong. I want first to reproduce your output. You said earlier it's easy to convert a series of tiff image into a mha file using SimpleRTK. Do you mean by writing a short program, or is it possible from the command line ? MG 2016-01-26 17:17 GMT-05:00 louie L : > Hi MG, > > > > Sometimes, the progressive deformation from the center of rotation to the > edge of the image is caused by wrong sdd/sid ratio. Such as change in the > geometry will lead to distortion of the image and wrong magnification. > > Maybe you can play with that parameter and report your result. > > > > Cheers, > > Louie > > > > Sent from Mail for > Windows 10 > > > > > *From: *Simon Rit > *Sent: *Tuesday, January 26, 2016 13:24 > *To: *MG Vallet > *Cc: *rtk-users at public.kitware.com > *Subject: *Re: [Rtk-users] Sophia beads reconstruction > > > > Hi, > > I think it's likely a problem with parameters. The best would be to obtain > them from the Matlab code they provide. > > Good luck, > > Simon > > > > On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > > Hi Simon, > > > > this was a point I missed. I had to do the log mapping. > > > > I must say, I do not use RTK from shell. I just plugged the objects > > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > > > MG > > > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > > > I really appreciate your insight. > > > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > > > Regards, > > mg > > > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > > Hi, > > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > > Good luck, > > Simon > > > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > > Thanks Cyril! > > going to carefully check my inputs and I give you some news. > > mgv > > > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > > This is a plastic tube filled with glass beads that has been scanned. > > > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > > > Regards, > > mgv > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 4 16:55:56 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 4 Jan 2016 16:55:56 -0500 Subject: [Rtk-users] feldkamp application Message-ID: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Tue Jan 5 03:25:50 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 05 Jan 2016 09:25:50 +0100 Subject: [Rtk-users] feldkamp application In-Reply-To: References: Message-ID: <568B7E0E.9030904@uclouvain.be> Hi, and happy new year :) You can use the dataset provided for the motion-compensated reconstruction : http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Hope it helps, Cyril On 01/04/2016 10:55 PM, MG Vallet wrote: > Happy new year! > > Does someone have a data set, other than quadric phantoms, to test the > fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 5 05:16:50 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 5 Jan 2016 11:16:50 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: Message-ID: <568B9812.40404@creatis.insa-lyon.fr> Hi, I forgot to cc this email to the mailing list, in answers to mgv. Simon -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit To: MG Vallet Hi, There are vendor-specific examples available on the wiki: http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction You also have real patient data for 4D CBCT, e.g. http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Simon On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 5 16:50:09 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 5 Jan 2016 16:50:09 -0500 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: <568B9812.40404@creatis.insa-lyon.fr> References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: Thanks, Cyril and Simon. These applications seemed complicated to me, but it's only data reading that is. By the way, the command rtkfieldofview had no effect in the varian case (no error message, nor output file). Otherwise, everything's OK. 2016-01-05 5:16 GMT-05:00 Simon Rit : > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp > application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit > To: MG > Vallet > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet wrote: > >> Happy new year! >> >> Does someone have a data set, other than quadric phantoms, to test the >> fdk module ? >> It would be fine to add one to the wiki page >> http://wiki.openrtk.org/index.php/Main_Page#Applications >> >> mgv >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Mon Jan 11 09:34:58 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Mon, 11 Jan 2016 15:34:58 +0100 Subject: [Rtk-users] Parker weighting In-Reply-To: <56743FCB.3040102@creatis.insa-lyon.fr> References: <56667F38.6040604@creatis.insa-lyon.fr> <56743FCB.3040102@creatis.insa-lyon.fr> Message-ID: Dear Simon, I am sorry for the late reply. I also wish you a happy new year. I will recheck if there is any error during generating projection images. The projections are generated from a volume with our simulation tool. However, I generated projections from the volume with rtkforwardprojections and I re-reconstructed the volume with rtkfdk. I did not get any artifacts. I will contact you soon, if I have some results. Thank you very much for your help. Shiras On Fri, Dec 18, 2015 at 6:18 PM, Simon Rit wrote: > Hi Shiras, > Sorry for the delayed answer, times are busy. The way RTK computes the > spanned arc is from the second projection angle to the before last > projection angle, i.e., in your case > 209.609216488925-11.6067737022482 > so it's a span of 199 degrees and your cone angle is indeed too large. > Like I said, this part of RTK is perfectible and there is no way to change > this but change the code. > However, the source of artefacts might be something else. On simulated > data, I tried: > rtkprojectshepploganphantom --like original_proj.mhd -g > geometry_parker_corr.xml -o proj.mha > rtkfdk -p . -r proj.mha -o fdk.mha -g geometry_parker_corr.xml > and the result is not that bad. What do you think? Can you show us a > snapshot if sg's wrong in your opinion? > Simon > > > On 09/12/2015 11:01, Shiras Abdurahman wrote: > > Dear Simon, > > I am attaching the mhd files of projections. > > With regards, > Shiras > > On Tue, Dec 8, 2015 at 6:17 PM, Simon Rit > wrote: > >> Hi, >> The geometry files look ok to me. What is the projection information? If >> you're still getting the same message as before, I think it's because you >> don't have enough data. If you send the mhd file of the projections (just >> the mhd, not the raw data), I can try to test it on simulated data to let >> you know my feeling. >> Simon >> >> On Tue, Dec 8, 2015 at 5:41 PM, Shiras Abdurahman < >> shiraska at gmail.com> wrote: >> >>> Dear Simon, >>> >>> I tried this option and unfortunately it did not work. I added zero >>> projections and modified geometry files. However, I am getting same >>> artifacts in the volume. Voxel values changed a little bit that indicates >>> during backprojection it still considers extreme projections. I am also >>> getting an output message same as before. >>> >>> I am attaching geometry files. >>> >>> With regards, >>> Shiras >>> >>> On Tue, Dec 8, 2015 at 10:15 AM, Simon Rit < >>> simon.rit at creatis.insa-lyon.fr> wrote: >>> >>>> So calling AddProjection before and after the loop with an adequate >>>> gantry_angle should work. >>>> Simon >>>> >>>> On Tue, Dec 8, 2015 at 9:52 AM, Shiras Abdurahman < >>>> shiraska at gmail.com> wrote: >>>> >>>>> Drear Simon, >>>>> >>>>> I generate the geometry with system geometry parameters and using >>>>> AddProjection method. >>>>> >>>>> Here is the code >>>>> >>>>> >>>>> rtk::ThreeDCircularProjectionGeometry::Pointer rtk_sys_geometry_; >>>>> rtk_sys_geometry_ = rtk::ThreeDCircularProjectionGeometry::New(); >>>>> for (uint16_t proj_index = 0; proj_index < num_projections_; >>>>> proj_index++) >>>>> { >>>>> >>>>> rtk_sys_geometry_->AddProjection(rtk_geom_params_.at(proj_index).sid_mm, >>>>> rtk_geom_params_.at(proj_index).sdd_mm, >>>>> rtk_geom_params_.at(proj_index).gantry_angle_deg, >>>>> rtk_geom_params_.at(proj_index).proj_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).proj_offset_y_mm, >>>>> rtk_geom_params_.at(proj_index).out_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).in_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).src_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).src_offset_y_mm); >>>>> } >>>>> >>>>> And then write to xml file. >>>>> >>>>> Shiras >>>>> >>>>> >>>>> >>>>> On Tue, Dec 8, 2015 at 9:23 AM, Simon Rit < >>>>> simon.rit at creatis.insa-lyon.fr> wrote: >>>>> >>>>>> Hi, >>>>>> rtkfdk.cxx just read the geometry from a file so the best is to >>>>>> modify the geometry file. How do you generate the geometry? >>>>>> For example, if you use rtksimulated geometry, let's say that you >>>>>> were using: >>>>>> rtksimulatedgeometry -n 200 -a 200 -o g.xml >>>>>> then you'll have to replace it with >>>>>> rtksimulatedgeometry -n 202 -a 202 -o g.xml -f -1 >>>>>> Don't forget to add dummy projection at the beginning and the end. If >>>>>> you use a more complex geometry, maybe SimpleRTK >>>>>> can be helpful >>>>>> (I'd use that) or you'd have to modify the cxx code to add these additional >>>>>> projections in the geometry and the projection stack. >>>>>> Simon >>>>>> >>>>>> >>>>>> On Tue, Dec 8, 2015 at 8:51 AM, Shiras Abdurahman < >>>>>> shiraska at gmail.com> wrote: >>>>>> >>>>>>> Dear Simon, >>>>>>> >>>>>>> Thanks a lot for the reply. Can you please inform me how can I set >>>>>>> where the arc starts? >>>>>>> Do I need to modify geometry also? >>>>>>> If you can point the line of code rtkfdk.cxx, it will be really >>>>>>> helpful. >>>>>>> >>>>>>> With regards, >>>>>>> Shiras >>>>>>> >>>>>>> On Tue, Dec 8, 2015 at 7:56 AM, Simon Rit < >>>>>>> simon.rit at creatis.insa-lyon.fr> >>>>>>> wrote: >>>>>>> >>>>>>>> Dear Shiras, >>>>>>>> Yes, for practical reasons the first and the last projections are >>>>>>>> set to 0 and the arc used in the Parker weighting starts between the first >>>>>>>> two projections and ends between the lasts two projections. There is a >>>>>>>> simple solution: add a projection at the beginning and the end of the arc, >>>>>>>> which can contain any pixel values but should be set where you want this >>>>>>>> arc to start. In the future, I think someone should once take the time to >>>>>>>> correct this but I haven't so far. I'll keep you posted on the mailing list >>>>>>>> when it's corrected. >>>>>>>> Simon >>>>>>>> >>>>>>>> On 07/12/2015 12:04, Shiras Abdurahman wrote: >>>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I am trying to reconstruct a volume from projection data generated >>>>>>>> with C-arm CT. There are 248 projections with an angular range of 199 >>>>>>>> degree. Technically, parker weighting should run without any problems. >>>>>>>> However, I am getting an output message that "You do not have enough data >>>>>>>> for proper parker weighting". After parker weighting, the two extreme >>>>>>>> projections (projection number 1 and 248) were completely zero and thus >>>>>>>> reconstructed volume contained artifacts. When I increased the angular >>>>>>>> range, this problem did not happen. How can I solve this problem without >>>>>>>> increasing angular range? Is there any threshold constant that I can change >>>>>>>> in command line or in my code? >>>>>>>> >>>>>>>> I really appreciate any help you can provide. >>>>>>>> >>>>>>>> With regards, >>>>>>>> Shiras >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 12 07:47:46 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 12 Jan 2016 13:47:46 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: <5694F5F2.4060702@creatis.insa-lyon.fr> Hi, There was a typo on the folder path (../Scan0 instead of Scan0). Was that the problem? I checked and it has the expected effect, i.e., setting to 0 everything outside the FOV. Simon On 05/01/2016 22:50, MG Vallet wrote: > Thanks, Cyril and Simon. > These applications seemed complicated to me, but it's only data > reading that is. > By the way, the command rtkfieldofview had no effect in the varian > case (no error message, nor output file). Otherwise, everything's OK. > > 2016-01-05 5:16 GMT-05:00 Simon Rit >: > > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- > Subject: Re: [Rtk-users] feldkamp application > Date: Tue, 5 Jan 2016 08:40:00 +0100 > From: Simon Rit > > To: MG Vallet > > > > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: > > Happy new year! > > Does someone have a data set, other than quadric phantoms, to > test the fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Wed Jan 13 07:42:45 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Wed, 13 Jan 2016 13:42:45 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry Message-ID: Dear all, I am trying to generate geometry xml file with rtkReg23ProjectionGeometry after decomposing projection matrix. One of the argument to the function AddReg23Projection is detector position. I assume that, it is the position vector of the center of the first pixel in world co-ordinates. This will be used for computing the projection offset parameters by projecting detector origin vector onto the u and v axis of the detector. If that is the case, do we need to change the offset parameters of each projection in the mhd file. Will this create problems during displaced detector correction? With regards, Shiras -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 13 13:31:23 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Jan 2016 19:31:23 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry In-Reply-To: References: Message-ID: <569697FB.1020804@creatis.insa-lyon.fr> Hi, Wrong assumption. It's the coordinate of point (0,0) in the coordinate of the projection image in the word coordinates, it's not the coordinate of the center of the first pixel. This is mentioned in the geometry description file on the wiki. You should not change the mhd parameters. If you want to account for offset parameters that change from projection to projection, you can put that offset in the computation of the detector position in world coordinates. Simon On 13/01/2016 13:42, Shiras Abdurahman wrote: > Dear all, > > I am trying to generate geometry xml file with > rtkReg23ProjectionGeometry after decomposing projection matrix. One of > the argument to the function AddReg23Projection is detector position. > I assume that, it is the position vector of the center of the first > pixel in world co-ordinates. This will be used for computing the > projection offset parameters by projecting detector origin vector onto > the u and v axis of the detector. If that is the case, do we need to > change the offset parameters of each projection in the mhd file. Will > this create problems during displaced detector correction? > > > With regards, > Shiras > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 10:19:12 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 10:19:12 -0500 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from https://zenodo.org/record/16539. This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts. I am not 100% sure I properly set the geometry parameters. Regards, mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sophiaBeadsCentralSlide.jpg Type: image/jpeg Size: 55394 bytes Desc: not available URL: From cyril.mory at uclouvain.be Tue Jan 19 10:33:02 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 19 Jan 2016 16:33:02 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: <569E572E.20203@uclouvain.be> Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit : > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% > sure I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users --- L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 14:02:45 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 14:02:45 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <569E572E.20203@uclouvain.be> References: <569E572E.20203@uclouvain.be> Message-ID: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > > ------------------------------ > [image: Avast logo] > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 20 03:33:47 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 20 Jan 2016 09:33:47 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > >> Hi, >> >> It looks like the geometry is wrong indeed, because I have never seen >> such artifacts. >> >> Hope that helps, >> Cyril >> >> >> Le 19/01/2016 16:19, MG Vallet a ?crit : >> >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data set from >> https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has been scanned. >> >> Attached is a view of the reconstructed central slice. It is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the proper term) >> >> My question is if these are simply expected artifacts. I am not 100% >> sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> >> ------------------------------ >> [image: Avast logo] >> >> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >> logiciel antivirus Avast. >> www.avast.com >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkfdk.sh Type: application/x-sh Size: 404 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: snapshot.jpg Type: image/jpeg Size: 95222 bytes Desc: not available URL: From mgvallet.pro at gmail.com Thu Jan 21 14:02:28 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 21 Jan 2016 14:02:28 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was SophiaBeads_512_averaged. Regarding the pre-processing mentioned by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > >> Thanks Cyril! >> going to carefully check my inputs and I give you some news. >> mgv >> >> 2016-01-19 10:33 GMT-05:00 Cyril Mory : >> >>> Hi, >>> >>> It looks like the geometry is wrong indeed, because I have never seen >>> such artifacts. >>> >>> Hope that helps, >>> Cyril >>> >>> >>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>> >>> Dear rtk-users, >>> >>> I applied the FDKConeBeamReconstructionFilter to a data set from >>> https://zenodo.org/record/16539. >>> This is a plastic tube filled with glass beads that has been scanned. >>> >>> Attached is a view of the reconstructed central slice. It is found that: >>> >>> 1. the beads are quickly deformed outside the center >>> 2. each one has a halo, or a shadow (dont know the proper term) >>> >>> My question is if these are simply expected artifacts. I am not 100% >>> sure I properly set the geometry parameters. >>> >>> Regards, >>> mgv >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >>> >>> ------------------------------ >>> [image: Avast logo] >>> >>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>> logiciel antivirus Avast. >>> www.avast.com >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_offset.jpg Type: image/jpeg Size: 52844 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Thu Jan 21 14:22:55 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Jan 2016 20:22:55 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: <56A1300F.1090509@creatis.insa-lyon.fr> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center > must effectively be offset (4.8 mm in both directions). For the > attached image, I also increases sdd and sid by a factor 1000, just in > case I would be wrong in units. It reduces the first default I pointed > out in my first message. Also note that my input dataset was > SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is > it as simple as the FDK filter assumes that the input is intensity, > but the dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit >: > > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems > that what is provided is directly the line integral. RTK will > process the tif images as if it were a photon count so I converted > the tif projections to mha to avoid this. For the conversion, I > used another piece of software but you can easily do the same > thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better > result. I have however a geometry problem. I think they provide a > Matlab piece of code to get the center of rotation. If you can run > it and find out what is this center, then you can use it to > configure the geometry better with the options --proj_iso_x and > --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet > wrote: > > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory >: > > Hi, > > It looks like the geometry is wrong indeed, because I have > never seen such artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data >> set from https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has >> been scanned. >> >> Attached is a view of the reconstructed central slice. It >> is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the >> proper term) >> >> My question is if these are simply expected artifacts. I >> am not 100% sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> >> http://public.kitware.com/mailman/listinfo/rtk-users > > > > ------------------------------------------------------------------------ > Avast logo > > L'absence de virus dans ce courrier ?lectronique a ?t? > v?rifi?e par le logiciel antivirus Avast. > www.avast.com > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 25 11:48:35 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 25 Jan 2016 11:48:35 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <56A1300F.1090509@creatis.insa-lyon.fr> References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > >> Hi, >> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >> is provided is directly the line integral. RTK will process the tif images >> as if it were a photon count so I converted the tif projections to mha to >> avoid this. For the conversion, I used another piece of software but you >> can easily do the same thing with SimpleRTK. >> Second, I used the enclosed script which gives me a much better result. I >> have however a geometry problem. I think they provide a Matlab piece of >> code to get the center of rotation. If you can run it and find out what is >> this center, then you can use it to configure the geometry better with the >> options --proj_iso_x and --proj_iso_y. >> Good luck, >> Simon >> >> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >> mgvallet.pro at gmail.com> wrote: >> >>> Thanks Cyril! >>> going to carefully check my inputs and I give you some news. >>> mgv >>> >>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>> cyril.mory at uclouvain.be>: >>> >>>> Hi, >>>> >>>> It looks like the geometry is wrong indeed, because I have never seen >>>> such artifacts. >>>> >>>> Hope that helps, >>>> Cyril >>>> >>>> >>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>> >>>> Dear rtk-users, >>>> >>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>> https://zenodo.org/record/16539. >>>> This is a plastic tube filled with glass beads that has been scanned. >>>> >>>> Attached is a view of the reconstructed central slice. It is found that: >>>> >>>> 1. the beads are quickly deformed outside the center >>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>> >>>> My question is if these are simply expected artifacts. I am not 100% >>>> sure I properly set the geometry parameters. >>>> >>>> Regards, >>>> mgv >>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> [image: Avast logo] >>>> >>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>> logiciel antivirus Avast. >>>> www.avast.com >>>> >>>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_log.jpg Type: image/jpeg Size: 17331 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 26 07:23:58 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Jan 2016 13:23:58 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > Hi Simon, > > this was a point I missed. I had to do the log mapping. > > I must say, I do not use RTK from shell. I just plugged the objects > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > MG > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > >> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the >> line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the >> projections and converts them depending on the type: for mha or mhd, it >> just reads it and nothing else. For tif, it assumes that I is passed, try >> to guess I0 (or gets it from the cmd line) and computes ln(I0/I). >> So from each tif projection, instead of letting them go through the >> ProjectionsReader in RTK, directly use the ImageReader, stack them and pass >> it to the reconstruction algorithm. In other words, if you use SimpleRTK, >> use ImageSeriesReader instead of ProjectionsReader. >> Regarding the geometry, it would be nice to be confident in the geometry >> parameters, maybe from their Matlab code? >> Simon >> >> >> On 21/01/2016 20:02, MG Vallet wrote: >> >> Hi Simon and Cyril, >> >> I really appreciate your insight. >> >> By examining the parameters of the acquisition, I saw that the center >> must effectively be offset (4.8 mm in both directions). For the attached >> image, I also increases sdd and sid by a factor 1000, just in case I would >> be wrong in units. It reduces the first default I pointed out in my first >> message. Also note that my input dataset was SophiaBeads_512_averaged. >> >> Regarding the pre-processing mentioned by Simon, I need more help. Is it >> as simple as the FDK filter assumes that the input is intensity, but the >> dataset provides -ln(I/I0) ? >> >> Regards, >> mg >> >> 2016-01-20 3:33 GMT-05:00 Simon Rit : >> >>> Hi, >>> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >>> is provided is directly the line integral. RTK will process the tif images >>> as if it were a photon count so I converted the tif projections to mha to >>> avoid this. For the conversion, I used another piece of software but you >>> can easily do the same thing with SimpleRTK. >>> Second, I used the enclosed script which gives me a much better result. >>> I have however a geometry problem. I think they provide a Matlab piece of >>> code to get the center of rotation. If you can run it and find out what is >>> this center, then you can use it to configure the geometry better with the >>> options --proj_iso_x and --proj_iso_y. >>> Good luck, >>> Simon >>> >>> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >>> mgvallet.pro at gmail.com> wrote: >>> >>>> Thanks Cyril! >>>> going to carefully check my inputs and I give you some news. >>>> mgv >>>> >>>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>>> cyril.mory at uclouvain.be>: >>>> >>>>> Hi, >>>>> >>>>> It looks like the geometry is wrong indeed, because I have never seen >>>>> such artifacts. >>>>> >>>>> Hope that helps, >>>>> Cyril >>>>> >>>>> >>>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>>> >>>>> Dear rtk-users, >>>>> >>>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>>> https://zenodo.org/record/16539. >>>>> This is a plastic tube filled with glass beads that has been scanned. >>>>> >>>>> Attached is a view of the reconstructed central slice. It is found >>>>> that: >>>>> >>>>> 1. the beads are quickly deformed outside the center >>>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>>> >>>>> My question is if these are simply expected artifacts. I am not 100% >>>>> sure I properly set the geometry parameters. >>>>> >>>>> Regards, >>>>> mgv >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> [image: Avast logo] >>>>> >>>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>>> logiciel antivirus Avast. >>>>> www.avast.com >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Jan 26 17:17:01 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 26 Jan 2016 23:17:01 +0100 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Hi MG, Sometimes, the progressive deformation from the center of rotation to the edge of the image is caused by wrong sdd/sid ratio. Such as change in the geometry will lead to distortion of the image and wrong magnification. Maybe you can play with that parameter and report your result. Cheers, Louie Sent from Mail for Windows 10 From: Simon Rit Sent: Tuesday, January 26, 2016 13:24 To: MG Vallet Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Sophia beads reconstruction Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and?ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was?SophiaBeads_512_averaged. Regarding the pre-processing?mentioned?by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit?: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from?https://zenodo.org/record/16539.? This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts.?I am not 100% sure I properly set the geometry parameters. Regards, mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. www.avast.com _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Thu Jan 28 16:27:15 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 28 Jan 2016 16:27:15 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: Louie, I played with sdd and sid, following your advise. But they have few effect, clearly less effect than proj_iso_x. And none of these parameters can significantly improve my result. Simon, I carefully checked every input data and I cant see what I did wrong. I want first to reproduce your output. You said earlier it's easy to convert a series of tiff image into a mha file using SimpleRTK. Do you mean by writing a short program, or is it possible from the command line ? MG 2016-01-26 17:17 GMT-05:00 louie L : > Hi MG, > > > > Sometimes, the progressive deformation from the center of rotation to the > edge of the image is caused by wrong sdd/sid ratio. Such as change in the > geometry will lead to distortion of the image and wrong magnification. > > Maybe you can play with that parameter and report your result. > > > > Cheers, > > Louie > > > > Sent from Mail for > Windows 10 > > > > > *From: *Simon Rit > *Sent: *Tuesday, January 26, 2016 13:24 > *To: *MG Vallet > *Cc: *rtk-users at public.kitware.com > *Subject: *Re: [Rtk-users] Sophia beads reconstruction > > > > Hi, > > I think it's likely a problem with parameters. The best would be to obtain > them from the Matlab code they provide. > > Good luck, > > Simon > > > > On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > > Hi Simon, > > > > this was a point I missed. I had to do the log mapping. > > > > I must say, I do not use RTK from shell. I just plugged the objects > > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > > > MG > > > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > > > I really appreciate your insight. > > > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > > > Regards, > > mg > > > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > > Hi, > > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > > Good luck, > > Simon > > > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > > Thanks Cyril! > > going to carefully check my inputs and I give you some news. > > mgv > > > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > > This is a plastic tube filled with glass beads that has been scanned. > > > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > > > Regards, > > mgv > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 4 16:55:56 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 4 Jan 2016 16:55:56 -0500 Subject: [Rtk-users] feldkamp application Message-ID: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Tue Jan 5 03:25:50 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 05 Jan 2016 09:25:50 +0100 Subject: [Rtk-users] feldkamp application In-Reply-To: References: Message-ID: <568B7E0E.9030904@uclouvain.be> Hi, and happy new year :) You can use the dataset provided for the motion-compensated reconstruction : http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Hope it helps, Cyril On 01/04/2016 10:55 PM, MG Vallet wrote: > Happy new year! > > Does someone have a data set, other than quadric phantoms, to test the > fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 5 05:16:50 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 5 Jan 2016 11:16:50 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: Message-ID: <568B9812.40404@creatis.insa-lyon.fr> Hi, I forgot to cc this email to the mailing list, in answers to mgv. Simon -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit To: MG Vallet Hi, There are vendor-specific examples available on the wiki: http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction You also have real patient data for 4D CBCT, e.g. http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Simon On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 5 16:50:09 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 5 Jan 2016 16:50:09 -0500 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: <568B9812.40404@creatis.insa-lyon.fr> References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: Thanks, Cyril and Simon. These applications seemed complicated to me, but it's only data reading that is. By the way, the command rtkfieldofview had no effect in the varian case (no error message, nor output file). Otherwise, everything's OK. 2016-01-05 5:16 GMT-05:00 Simon Rit : > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp > application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit > To: MG > Vallet > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet wrote: > >> Happy new year! >> >> Does someone have a data set, other than quadric phantoms, to test the >> fdk module ? >> It would be fine to add one to the wiki page >> http://wiki.openrtk.org/index.php/Main_Page#Applications >> >> mgv >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Mon Jan 11 09:34:58 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Mon, 11 Jan 2016 15:34:58 +0100 Subject: [Rtk-users] Parker weighting In-Reply-To: <56743FCB.3040102@creatis.insa-lyon.fr> References: <56667F38.6040604@creatis.insa-lyon.fr> <56743FCB.3040102@creatis.insa-lyon.fr> Message-ID: Dear Simon, I am sorry for the late reply. I also wish you a happy new year. I will recheck if there is any error during generating projection images. The projections are generated from a volume with our simulation tool. However, I generated projections from the volume with rtkforwardprojections and I re-reconstructed the volume with rtkfdk. I did not get any artifacts. I will contact you soon, if I have some results. Thank you very much for your help. Shiras On Fri, Dec 18, 2015 at 6:18 PM, Simon Rit wrote: > Hi Shiras, > Sorry for the delayed answer, times are busy. The way RTK computes the > spanned arc is from the second projection angle to the before last > projection angle, i.e., in your case > 209.609216488925-11.6067737022482 > so it's a span of 199 degrees and your cone angle is indeed too large. > Like I said, this part of RTK is perfectible and there is no way to change > this but change the code. > However, the source of artefacts might be something else. On simulated > data, I tried: > rtkprojectshepploganphantom --like original_proj.mhd -g > geometry_parker_corr.xml -o proj.mha > rtkfdk -p . -r proj.mha -o fdk.mha -g geometry_parker_corr.xml > and the result is not that bad. What do you think? Can you show us a > snapshot if sg's wrong in your opinion? > Simon > > > On 09/12/2015 11:01, Shiras Abdurahman wrote: > > Dear Simon, > > I am attaching the mhd files of projections. > > With regards, > Shiras > > On Tue, Dec 8, 2015 at 6:17 PM, Simon Rit > wrote: > >> Hi, >> The geometry files look ok to me. What is the projection information? If >> you're still getting the same message as before, I think it's because you >> don't have enough data. If you send the mhd file of the projections (just >> the mhd, not the raw data), I can try to test it on simulated data to let >> you know my feeling. >> Simon >> >> On Tue, Dec 8, 2015 at 5:41 PM, Shiras Abdurahman < >> shiraska at gmail.com> wrote: >> >>> Dear Simon, >>> >>> I tried this option and unfortunately it did not work. I added zero >>> projections and modified geometry files. However, I am getting same >>> artifacts in the volume. Voxel values changed a little bit that indicates >>> during backprojection it still considers extreme projections. I am also >>> getting an output message same as before. >>> >>> I am attaching geometry files. >>> >>> With regards, >>> Shiras >>> >>> On Tue, Dec 8, 2015 at 10:15 AM, Simon Rit < >>> simon.rit at creatis.insa-lyon.fr> wrote: >>> >>>> So calling AddProjection before and after the loop with an adequate >>>> gantry_angle should work. >>>> Simon >>>> >>>> On Tue, Dec 8, 2015 at 9:52 AM, Shiras Abdurahman < >>>> shiraska at gmail.com> wrote: >>>> >>>>> Drear Simon, >>>>> >>>>> I generate the geometry with system geometry parameters and using >>>>> AddProjection method. >>>>> >>>>> Here is the code >>>>> >>>>> >>>>> rtk::ThreeDCircularProjectionGeometry::Pointer rtk_sys_geometry_; >>>>> rtk_sys_geometry_ = rtk::ThreeDCircularProjectionGeometry::New(); >>>>> for (uint16_t proj_index = 0; proj_index < num_projections_; >>>>> proj_index++) >>>>> { >>>>> >>>>> rtk_sys_geometry_->AddProjection(rtk_geom_params_.at(proj_index).sid_mm, >>>>> rtk_geom_params_.at(proj_index).sdd_mm, >>>>> rtk_geom_params_.at(proj_index).gantry_angle_deg, >>>>> rtk_geom_params_.at(proj_index).proj_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).proj_offset_y_mm, >>>>> rtk_geom_params_.at(proj_index).out_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).in_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).src_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).src_offset_y_mm); >>>>> } >>>>> >>>>> And then write to xml file. >>>>> >>>>> Shiras >>>>> >>>>> >>>>> >>>>> On Tue, Dec 8, 2015 at 9:23 AM, Simon Rit < >>>>> simon.rit at creatis.insa-lyon.fr> wrote: >>>>> >>>>>> Hi, >>>>>> rtkfdk.cxx just read the geometry from a file so the best is to >>>>>> modify the geometry file. How do you generate the geometry? >>>>>> For example, if you use rtksimulated geometry, let's say that you >>>>>> were using: >>>>>> rtksimulatedgeometry -n 200 -a 200 -o g.xml >>>>>> then you'll have to replace it with >>>>>> rtksimulatedgeometry -n 202 -a 202 -o g.xml -f -1 >>>>>> Don't forget to add dummy projection at the beginning and the end. If >>>>>> you use a more complex geometry, maybe SimpleRTK >>>>>> can be helpful >>>>>> (I'd use that) or you'd have to modify the cxx code to add these additional >>>>>> projections in the geometry and the projection stack. >>>>>> Simon >>>>>> >>>>>> >>>>>> On Tue, Dec 8, 2015 at 8:51 AM, Shiras Abdurahman < >>>>>> shiraska at gmail.com> wrote: >>>>>> >>>>>>> Dear Simon, >>>>>>> >>>>>>> Thanks a lot for the reply. Can you please inform me how can I set >>>>>>> where the arc starts? >>>>>>> Do I need to modify geometry also? >>>>>>> If you can point the line of code rtkfdk.cxx, it will be really >>>>>>> helpful. >>>>>>> >>>>>>> With regards, >>>>>>> Shiras >>>>>>> >>>>>>> On Tue, Dec 8, 2015 at 7:56 AM, Simon Rit < >>>>>>> simon.rit at creatis.insa-lyon.fr> >>>>>>> wrote: >>>>>>> >>>>>>>> Dear Shiras, >>>>>>>> Yes, for practical reasons the first and the last projections are >>>>>>>> set to 0 and the arc used in the Parker weighting starts between the first >>>>>>>> two projections and ends between the lasts two projections. There is a >>>>>>>> simple solution: add a projection at the beginning and the end of the arc, >>>>>>>> which can contain any pixel values but should be set where you want this >>>>>>>> arc to start. In the future, I think someone should once take the time to >>>>>>>> correct this but I haven't so far. I'll keep you posted on the mailing list >>>>>>>> when it's corrected. >>>>>>>> Simon >>>>>>>> >>>>>>>> On 07/12/2015 12:04, Shiras Abdurahman wrote: >>>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I am trying to reconstruct a volume from projection data generated >>>>>>>> with C-arm CT. There are 248 projections with an angular range of 199 >>>>>>>> degree. Technically, parker weighting should run without any problems. >>>>>>>> However, I am getting an output message that "You do not have enough data >>>>>>>> for proper parker weighting". After parker weighting, the two extreme >>>>>>>> projections (projection number 1 and 248) were completely zero and thus >>>>>>>> reconstructed volume contained artifacts. When I increased the angular >>>>>>>> range, this problem did not happen. How can I solve this problem without >>>>>>>> increasing angular range? Is there any threshold constant that I can change >>>>>>>> in command line or in my code? >>>>>>>> >>>>>>>> I really appreciate any help you can provide. >>>>>>>> >>>>>>>> With regards, >>>>>>>> Shiras >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 12 07:47:46 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 12 Jan 2016 13:47:46 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: <5694F5F2.4060702@creatis.insa-lyon.fr> Hi, There was a typo on the folder path (../Scan0 instead of Scan0). Was that the problem? I checked and it has the expected effect, i.e., setting to 0 everything outside the FOV. Simon On 05/01/2016 22:50, MG Vallet wrote: > Thanks, Cyril and Simon. > These applications seemed complicated to me, but it's only data > reading that is. > By the way, the command rtkfieldofview had no effect in the varian > case (no error message, nor output file). Otherwise, everything's OK. > > 2016-01-05 5:16 GMT-05:00 Simon Rit >: > > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- > Subject: Re: [Rtk-users] feldkamp application > Date: Tue, 5 Jan 2016 08:40:00 +0100 > From: Simon Rit > > To: MG Vallet > > > > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: > > Happy new year! > > Does someone have a data set, other than quadric phantoms, to > test the fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Wed Jan 13 07:42:45 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Wed, 13 Jan 2016 13:42:45 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry Message-ID: Dear all, I am trying to generate geometry xml file with rtkReg23ProjectionGeometry after decomposing projection matrix. One of the argument to the function AddReg23Projection is detector position. I assume that, it is the position vector of the center of the first pixel in world co-ordinates. This will be used for computing the projection offset parameters by projecting detector origin vector onto the u and v axis of the detector. If that is the case, do we need to change the offset parameters of each projection in the mhd file. Will this create problems during displaced detector correction? With regards, Shiras -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 13 13:31:23 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Jan 2016 19:31:23 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry In-Reply-To: References: Message-ID: <569697FB.1020804@creatis.insa-lyon.fr> Hi, Wrong assumption. It's the coordinate of point (0,0) in the coordinate of the projection image in the word coordinates, it's not the coordinate of the center of the first pixel. This is mentioned in the geometry description file on the wiki. You should not change the mhd parameters. If you want to account for offset parameters that change from projection to projection, you can put that offset in the computation of the detector position in world coordinates. Simon On 13/01/2016 13:42, Shiras Abdurahman wrote: > Dear all, > > I am trying to generate geometry xml file with > rtkReg23ProjectionGeometry after decomposing projection matrix. One of > the argument to the function AddReg23Projection is detector position. > I assume that, it is the position vector of the center of the first > pixel in world co-ordinates. This will be used for computing the > projection offset parameters by projecting detector origin vector onto > the u and v axis of the detector. If that is the case, do we need to > change the offset parameters of each projection in the mhd file. Will > this create problems during displaced detector correction? > > > With regards, > Shiras > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 10:19:12 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 10:19:12 -0500 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from https://zenodo.org/record/16539. This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts. I am not 100% sure I properly set the geometry parameters. Regards, mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sophiaBeadsCentralSlide.jpg Type: image/jpeg Size: 55394 bytes Desc: not available URL: From cyril.mory at uclouvain.be Tue Jan 19 10:33:02 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 19 Jan 2016 16:33:02 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: <569E572E.20203@uclouvain.be> Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit : > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% > sure I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users --- L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 14:02:45 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 14:02:45 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <569E572E.20203@uclouvain.be> References: <569E572E.20203@uclouvain.be> Message-ID: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > > ------------------------------ > [image: Avast logo] > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 20 03:33:47 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 20 Jan 2016 09:33:47 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > >> Hi, >> >> It looks like the geometry is wrong indeed, because I have never seen >> such artifacts. >> >> Hope that helps, >> Cyril >> >> >> Le 19/01/2016 16:19, MG Vallet a ?crit : >> >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data set from >> https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has been scanned. >> >> Attached is a view of the reconstructed central slice. It is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the proper term) >> >> My question is if these are simply expected artifacts. I am not 100% >> sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> >> ------------------------------ >> [image: Avast logo] >> >> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >> logiciel antivirus Avast. >> www.avast.com >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkfdk.sh Type: application/x-sh Size: 404 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: snapshot.jpg Type: image/jpeg Size: 95222 bytes Desc: not available URL: From mgvallet.pro at gmail.com Thu Jan 21 14:02:28 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 21 Jan 2016 14:02:28 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was SophiaBeads_512_averaged. Regarding the pre-processing mentioned by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > >> Thanks Cyril! >> going to carefully check my inputs and I give you some news. >> mgv >> >> 2016-01-19 10:33 GMT-05:00 Cyril Mory : >> >>> Hi, >>> >>> It looks like the geometry is wrong indeed, because I have never seen >>> such artifacts. >>> >>> Hope that helps, >>> Cyril >>> >>> >>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>> >>> Dear rtk-users, >>> >>> I applied the FDKConeBeamReconstructionFilter to a data set from >>> https://zenodo.org/record/16539. >>> This is a plastic tube filled with glass beads that has been scanned. >>> >>> Attached is a view of the reconstructed central slice. It is found that: >>> >>> 1. the beads are quickly deformed outside the center >>> 2. each one has a halo, or a shadow (dont know the proper term) >>> >>> My question is if these are simply expected artifacts. I am not 100% >>> sure I properly set the geometry parameters. >>> >>> Regards, >>> mgv >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >>> >>> ------------------------------ >>> [image: Avast logo] >>> >>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>> logiciel antivirus Avast. >>> www.avast.com >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_offset.jpg Type: image/jpeg Size: 52844 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Thu Jan 21 14:22:55 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Jan 2016 20:22:55 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: <56A1300F.1090509@creatis.insa-lyon.fr> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center > must effectively be offset (4.8 mm in both directions). For the > attached image, I also increases sdd and sid by a factor 1000, just in > case I would be wrong in units. It reduces the first default I pointed > out in my first message. Also note that my input dataset was > SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is > it as simple as the FDK filter assumes that the input is intensity, > but the dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit >: > > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems > that what is provided is directly the line integral. RTK will > process the tif images as if it were a photon count so I converted > the tif projections to mha to avoid this. For the conversion, I > used another piece of software but you can easily do the same > thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better > result. I have however a geometry problem. I think they provide a > Matlab piece of code to get the center of rotation. If you can run > it and find out what is this center, then you can use it to > configure the geometry better with the options --proj_iso_x and > --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet > wrote: > > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory >: > > Hi, > > It looks like the geometry is wrong indeed, because I have > never seen such artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data >> set from https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has >> been scanned. >> >> Attached is a view of the reconstructed central slice. It >> is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the >> proper term) >> >> My question is if these are simply expected artifacts. I >> am not 100% sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> >> http://public.kitware.com/mailman/listinfo/rtk-users > > > > ------------------------------------------------------------------------ > Avast logo > > L'absence de virus dans ce courrier ?lectronique a ?t? > v?rifi?e par le logiciel antivirus Avast. > www.avast.com > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 25 11:48:35 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 25 Jan 2016 11:48:35 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <56A1300F.1090509@creatis.insa-lyon.fr> References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > >> Hi, >> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >> is provided is directly the line integral. RTK will process the tif images >> as if it were a photon count so I converted the tif projections to mha to >> avoid this. For the conversion, I used another piece of software but you >> can easily do the same thing with SimpleRTK. >> Second, I used the enclosed script which gives me a much better result. I >> have however a geometry problem. I think they provide a Matlab piece of >> code to get the center of rotation. If you can run it and find out what is >> this center, then you can use it to configure the geometry better with the >> options --proj_iso_x and --proj_iso_y. >> Good luck, >> Simon >> >> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >> mgvallet.pro at gmail.com> wrote: >> >>> Thanks Cyril! >>> going to carefully check my inputs and I give you some news. >>> mgv >>> >>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>> cyril.mory at uclouvain.be>: >>> >>>> Hi, >>>> >>>> It looks like the geometry is wrong indeed, because I have never seen >>>> such artifacts. >>>> >>>> Hope that helps, >>>> Cyril >>>> >>>> >>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>> >>>> Dear rtk-users, >>>> >>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>> https://zenodo.org/record/16539. >>>> This is a plastic tube filled with glass beads that has been scanned. >>>> >>>> Attached is a view of the reconstructed central slice. It is found that: >>>> >>>> 1. the beads are quickly deformed outside the center >>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>> >>>> My question is if these are simply expected artifacts. I am not 100% >>>> sure I properly set the geometry parameters. >>>> >>>> Regards, >>>> mgv >>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> [image: Avast logo] >>>> >>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>> logiciel antivirus Avast. >>>> www.avast.com >>>> >>>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_log.jpg Type: image/jpeg Size: 17331 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 26 07:23:58 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Jan 2016 13:23:58 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > Hi Simon, > > this was a point I missed. I had to do the log mapping. > > I must say, I do not use RTK from shell. I just plugged the objects > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > MG > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > >> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the >> line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the >> projections and converts them depending on the type: for mha or mhd, it >> just reads it and nothing else. For tif, it assumes that I is passed, try >> to guess I0 (or gets it from the cmd line) and computes ln(I0/I). >> So from each tif projection, instead of letting them go through the >> ProjectionsReader in RTK, directly use the ImageReader, stack them and pass >> it to the reconstruction algorithm. In other words, if you use SimpleRTK, >> use ImageSeriesReader instead of ProjectionsReader. >> Regarding the geometry, it would be nice to be confident in the geometry >> parameters, maybe from their Matlab code? >> Simon >> >> >> On 21/01/2016 20:02, MG Vallet wrote: >> >> Hi Simon and Cyril, >> >> I really appreciate your insight. >> >> By examining the parameters of the acquisition, I saw that the center >> must effectively be offset (4.8 mm in both directions). For the attached >> image, I also increases sdd and sid by a factor 1000, just in case I would >> be wrong in units. It reduces the first default I pointed out in my first >> message. Also note that my input dataset was SophiaBeads_512_averaged. >> >> Regarding the pre-processing mentioned by Simon, I need more help. Is it >> as simple as the FDK filter assumes that the input is intensity, but the >> dataset provides -ln(I/I0) ? >> >> Regards, >> mg >> >> 2016-01-20 3:33 GMT-05:00 Simon Rit : >> >>> Hi, >>> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >>> is provided is directly the line integral. RTK will process the tif images >>> as if it were a photon count so I converted the tif projections to mha to >>> avoid this. For the conversion, I used another piece of software but you >>> can easily do the same thing with SimpleRTK. >>> Second, I used the enclosed script which gives me a much better result. >>> I have however a geometry problem. I think they provide a Matlab piece of >>> code to get the center of rotation. If you can run it and find out what is >>> this center, then you can use it to configure the geometry better with the >>> options --proj_iso_x and --proj_iso_y. >>> Good luck, >>> Simon >>> >>> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >>> mgvallet.pro at gmail.com> wrote: >>> >>>> Thanks Cyril! >>>> going to carefully check my inputs and I give you some news. >>>> mgv >>>> >>>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>>> cyril.mory at uclouvain.be>: >>>> >>>>> Hi, >>>>> >>>>> It looks like the geometry is wrong indeed, because I have never seen >>>>> such artifacts. >>>>> >>>>> Hope that helps, >>>>> Cyril >>>>> >>>>> >>>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>>> >>>>> Dear rtk-users, >>>>> >>>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>>> https://zenodo.org/record/16539. >>>>> This is a plastic tube filled with glass beads that has been scanned. >>>>> >>>>> Attached is a view of the reconstructed central slice. It is found >>>>> that: >>>>> >>>>> 1. the beads are quickly deformed outside the center >>>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>>> >>>>> My question is if these are simply expected artifacts. I am not 100% >>>>> sure I properly set the geometry parameters. >>>>> >>>>> Regards, >>>>> mgv >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> [image: Avast logo] >>>>> >>>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>>> logiciel antivirus Avast. >>>>> www.avast.com >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Jan 26 17:17:01 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 26 Jan 2016 23:17:01 +0100 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Hi MG, Sometimes, the progressive deformation from the center of rotation to the edge of the image is caused by wrong sdd/sid ratio. Such as change in the geometry will lead to distortion of the image and wrong magnification. Maybe you can play with that parameter and report your result. Cheers, Louie Sent from Mail for Windows 10 From: Simon Rit Sent: Tuesday, January 26, 2016 13:24 To: MG Vallet Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Sophia beads reconstruction Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and?ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was?SophiaBeads_512_averaged. Regarding the pre-processing?mentioned?by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit?: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from?https://zenodo.org/record/16539.? This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts.?I am not 100% sure I properly set the geometry parameters. Regards, mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. www.avast.com _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Thu Jan 28 16:27:15 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 28 Jan 2016 16:27:15 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: Louie, I played with sdd and sid, following your advise. But they have few effect, clearly less effect than proj_iso_x. And none of these parameters can significantly improve my result. Simon, I carefully checked every input data and I cant see what I did wrong. I want first to reproduce your output. You said earlier it's easy to convert a series of tiff image into a mha file using SimpleRTK. Do you mean by writing a short program, or is it possible from the command line ? MG 2016-01-26 17:17 GMT-05:00 louie L : > Hi MG, > > > > Sometimes, the progressive deformation from the center of rotation to the > edge of the image is caused by wrong sdd/sid ratio. Such as change in the > geometry will lead to distortion of the image and wrong magnification. > > Maybe you can play with that parameter and report your result. > > > > Cheers, > > Louie > > > > Sent from Mail for > Windows 10 > > > > > *From: *Simon Rit > *Sent: *Tuesday, January 26, 2016 13:24 > *To: *MG Vallet > *Cc: *rtk-users at public.kitware.com > *Subject: *Re: [Rtk-users] Sophia beads reconstruction > > > > Hi, > > I think it's likely a problem with parameters. The best would be to obtain > them from the Matlab code they provide. > > Good luck, > > Simon > > > > On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > > Hi Simon, > > > > this was a point I missed. I had to do the log mapping. > > > > I must say, I do not use RTK from shell. I just plugged the objects > > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > > > MG > > > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > > > I really appreciate your insight. > > > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > > > Regards, > > mg > > > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > > Hi, > > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > > Good luck, > > Simon > > > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > > Thanks Cyril! > > going to carefully check my inputs and I give you some news. > > mgv > > > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > > This is a plastic tube filled with glass beads that has been scanned. > > > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > > > Regards, > > mgv > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 4 16:55:56 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 4 Jan 2016 16:55:56 -0500 Subject: [Rtk-users] feldkamp application Message-ID: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Tue Jan 5 03:25:50 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 05 Jan 2016 09:25:50 +0100 Subject: [Rtk-users] feldkamp application In-Reply-To: References: Message-ID: <568B7E0E.9030904@uclouvain.be> Hi, and happy new year :) You can use the dataset provided for the motion-compensated reconstruction : http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Hope it helps, Cyril On 01/04/2016 10:55 PM, MG Vallet wrote: > Happy new year! > > Does someone have a data set, other than quadric phantoms, to test the > fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 5 05:16:50 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 5 Jan 2016 11:16:50 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: Message-ID: <568B9812.40404@creatis.insa-lyon.fr> Hi, I forgot to cc this email to the mailing list, in answers to mgv. Simon -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit To: MG Vallet Hi, There are vendor-specific examples available on the wiki: http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction You also have real patient data for 4D CBCT, e.g. http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Simon On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 5 16:50:09 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 5 Jan 2016 16:50:09 -0500 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: <568B9812.40404@creatis.insa-lyon.fr> References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: Thanks, Cyril and Simon. These applications seemed complicated to me, but it's only data reading that is. By the way, the command rtkfieldofview had no effect in the varian case (no error message, nor output file). Otherwise, everything's OK. 2016-01-05 5:16 GMT-05:00 Simon Rit : > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp > application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit > To: MG > Vallet > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet wrote: > >> Happy new year! >> >> Does someone have a data set, other than quadric phantoms, to test the >> fdk module ? >> It would be fine to add one to the wiki page >> http://wiki.openrtk.org/index.php/Main_Page#Applications >> >> mgv >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Mon Jan 11 09:34:58 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Mon, 11 Jan 2016 15:34:58 +0100 Subject: [Rtk-users] Parker weighting In-Reply-To: <56743FCB.3040102@creatis.insa-lyon.fr> References: <56667F38.6040604@creatis.insa-lyon.fr> <56743FCB.3040102@creatis.insa-lyon.fr> Message-ID: Dear Simon, I am sorry for the late reply. I also wish you a happy new year. I will recheck if there is any error during generating projection images. The projections are generated from a volume with our simulation tool. However, I generated projections from the volume with rtkforwardprojections and I re-reconstructed the volume with rtkfdk. I did not get any artifacts. I will contact you soon, if I have some results. Thank you very much for your help. Shiras On Fri, Dec 18, 2015 at 6:18 PM, Simon Rit wrote: > Hi Shiras, > Sorry for the delayed answer, times are busy. The way RTK computes the > spanned arc is from the second projection angle to the before last > projection angle, i.e., in your case > 209.609216488925-11.6067737022482 > so it's a span of 199 degrees and your cone angle is indeed too large. > Like I said, this part of RTK is perfectible and there is no way to change > this but change the code. > However, the source of artefacts might be something else. On simulated > data, I tried: > rtkprojectshepploganphantom --like original_proj.mhd -g > geometry_parker_corr.xml -o proj.mha > rtkfdk -p . -r proj.mha -o fdk.mha -g geometry_parker_corr.xml > and the result is not that bad. What do you think? Can you show us a > snapshot if sg's wrong in your opinion? > Simon > > > On 09/12/2015 11:01, Shiras Abdurahman wrote: > > Dear Simon, > > I am attaching the mhd files of projections. > > With regards, > Shiras > > On Tue, Dec 8, 2015 at 6:17 PM, Simon Rit > wrote: > >> Hi, >> The geometry files look ok to me. What is the projection information? If >> you're still getting the same message as before, I think it's because you >> don't have enough data. If you send the mhd file of the projections (just >> the mhd, not the raw data), I can try to test it on simulated data to let >> you know my feeling. >> Simon >> >> On Tue, Dec 8, 2015 at 5:41 PM, Shiras Abdurahman < >> shiraska at gmail.com> wrote: >> >>> Dear Simon, >>> >>> I tried this option and unfortunately it did not work. I added zero >>> projections and modified geometry files. However, I am getting same >>> artifacts in the volume. Voxel values changed a little bit that indicates >>> during backprojection it still considers extreme projections. I am also >>> getting an output message same as before. >>> >>> I am attaching geometry files. >>> >>> With regards, >>> Shiras >>> >>> On Tue, Dec 8, 2015 at 10:15 AM, Simon Rit < >>> simon.rit at creatis.insa-lyon.fr> wrote: >>> >>>> So calling AddProjection before and after the loop with an adequate >>>> gantry_angle should work. >>>> Simon >>>> >>>> On Tue, Dec 8, 2015 at 9:52 AM, Shiras Abdurahman < >>>> shiraska at gmail.com> wrote: >>>> >>>>> Drear Simon, >>>>> >>>>> I generate the geometry with system geometry parameters and using >>>>> AddProjection method. >>>>> >>>>> Here is the code >>>>> >>>>> >>>>> rtk::ThreeDCircularProjectionGeometry::Pointer rtk_sys_geometry_; >>>>> rtk_sys_geometry_ = rtk::ThreeDCircularProjectionGeometry::New(); >>>>> for (uint16_t proj_index = 0; proj_index < num_projections_; >>>>> proj_index++) >>>>> { >>>>> >>>>> rtk_sys_geometry_->AddProjection(rtk_geom_params_.at(proj_index).sid_mm, >>>>> rtk_geom_params_.at(proj_index).sdd_mm, >>>>> rtk_geom_params_.at(proj_index).gantry_angle_deg, >>>>> rtk_geom_params_.at(proj_index).proj_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).proj_offset_y_mm, >>>>> rtk_geom_params_.at(proj_index).out_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).in_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).src_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).src_offset_y_mm); >>>>> } >>>>> >>>>> And then write to xml file. >>>>> >>>>> Shiras >>>>> >>>>> >>>>> >>>>> On Tue, Dec 8, 2015 at 9:23 AM, Simon Rit < >>>>> simon.rit at creatis.insa-lyon.fr> wrote: >>>>> >>>>>> Hi, >>>>>> rtkfdk.cxx just read the geometry from a file so the best is to >>>>>> modify the geometry file. How do you generate the geometry? >>>>>> For example, if you use rtksimulated geometry, let's say that you >>>>>> were using: >>>>>> rtksimulatedgeometry -n 200 -a 200 -o g.xml >>>>>> then you'll have to replace it with >>>>>> rtksimulatedgeometry -n 202 -a 202 -o g.xml -f -1 >>>>>> Don't forget to add dummy projection at the beginning and the end. If >>>>>> you use a more complex geometry, maybe SimpleRTK >>>>>> can be helpful >>>>>> (I'd use that) or you'd have to modify the cxx code to add these additional >>>>>> projections in the geometry and the projection stack. >>>>>> Simon >>>>>> >>>>>> >>>>>> On Tue, Dec 8, 2015 at 8:51 AM, Shiras Abdurahman < >>>>>> shiraska at gmail.com> wrote: >>>>>> >>>>>>> Dear Simon, >>>>>>> >>>>>>> Thanks a lot for the reply. Can you please inform me how can I set >>>>>>> where the arc starts? >>>>>>> Do I need to modify geometry also? >>>>>>> If you can point the line of code rtkfdk.cxx, it will be really >>>>>>> helpful. >>>>>>> >>>>>>> With regards, >>>>>>> Shiras >>>>>>> >>>>>>> On Tue, Dec 8, 2015 at 7:56 AM, Simon Rit < >>>>>>> simon.rit at creatis.insa-lyon.fr> >>>>>>> wrote: >>>>>>> >>>>>>>> Dear Shiras, >>>>>>>> Yes, for practical reasons the first and the last projections are >>>>>>>> set to 0 and the arc used in the Parker weighting starts between the first >>>>>>>> two projections and ends between the lasts two projections. There is a >>>>>>>> simple solution: add a projection at the beginning and the end of the arc, >>>>>>>> which can contain any pixel values but should be set where you want this >>>>>>>> arc to start. In the future, I think someone should once take the time to >>>>>>>> correct this but I haven't so far. I'll keep you posted on the mailing list >>>>>>>> when it's corrected. >>>>>>>> Simon >>>>>>>> >>>>>>>> On 07/12/2015 12:04, Shiras Abdurahman wrote: >>>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I am trying to reconstruct a volume from projection data generated >>>>>>>> with C-arm CT. There are 248 projections with an angular range of 199 >>>>>>>> degree. Technically, parker weighting should run without any problems. >>>>>>>> However, I am getting an output message that "You do not have enough data >>>>>>>> for proper parker weighting". After parker weighting, the two extreme >>>>>>>> projections (projection number 1 and 248) were completely zero and thus >>>>>>>> reconstructed volume contained artifacts. When I increased the angular >>>>>>>> range, this problem did not happen. How can I solve this problem without >>>>>>>> increasing angular range? Is there any threshold constant that I can change >>>>>>>> in command line or in my code? >>>>>>>> >>>>>>>> I really appreciate any help you can provide. >>>>>>>> >>>>>>>> With regards, >>>>>>>> Shiras >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 12 07:47:46 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 12 Jan 2016 13:47:46 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: <5694F5F2.4060702@creatis.insa-lyon.fr> Hi, There was a typo on the folder path (../Scan0 instead of Scan0). Was that the problem? I checked and it has the expected effect, i.e., setting to 0 everything outside the FOV. Simon On 05/01/2016 22:50, MG Vallet wrote: > Thanks, Cyril and Simon. > These applications seemed complicated to me, but it's only data > reading that is. > By the way, the command rtkfieldofview had no effect in the varian > case (no error message, nor output file). Otherwise, everything's OK. > > 2016-01-05 5:16 GMT-05:00 Simon Rit >: > > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- > Subject: Re: [Rtk-users] feldkamp application > Date: Tue, 5 Jan 2016 08:40:00 +0100 > From: Simon Rit > > To: MG Vallet > > > > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: > > Happy new year! > > Does someone have a data set, other than quadric phantoms, to > test the fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Wed Jan 13 07:42:45 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Wed, 13 Jan 2016 13:42:45 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry Message-ID: Dear all, I am trying to generate geometry xml file with rtkReg23ProjectionGeometry after decomposing projection matrix. One of the argument to the function AddReg23Projection is detector position. I assume that, it is the position vector of the center of the first pixel in world co-ordinates. This will be used for computing the projection offset parameters by projecting detector origin vector onto the u and v axis of the detector. If that is the case, do we need to change the offset parameters of each projection in the mhd file. Will this create problems during displaced detector correction? With regards, Shiras -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 13 13:31:23 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Jan 2016 19:31:23 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry In-Reply-To: References: Message-ID: <569697FB.1020804@creatis.insa-lyon.fr> Hi, Wrong assumption. It's the coordinate of point (0,0) in the coordinate of the projection image in the word coordinates, it's not the coordinate of the center of the first pixel. This is mentioned in the geometry description file on the wiki. You should not change the mhd parameters. If you want to account for offset parameters that change from projection to projection, you can put that offset in the computation of the detector position in world coordinates. Simon On 13/01/2016 13:42, Shiras Abdurahman wrote: > Dear all, > > I am trying to generate geometry xml file with > rtkReg23ProjectionGeometry after decomposing projection matrix. One of > the argument to the function AddReg23Projection is detector position. > I assume that, it is the position vector of the center of the first > pixel in world co-ordinates. This will be used for computing the > projection offset parameters by projecting detector origin vector onto > the u and v axis of the detector. If that is the case, do we need to > change the offset parameters of each projection in the mhd file. Will > this create problems during displaced detector correction? > > > With regards, > Shiras > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 10:19:12 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 10:19:12 -0500 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from https://zenodo.org/record/16539. This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts. I am not 100% sure I properly set the geometry parameters. Regards, mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sophiaBeadsCentralSlide.jpg Type: image/jpeg Size: 55394 bytes Desc: not available URL: From cyril.mory at uclouvain.be Tue Jan 19 10:33:02 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 19 Jan 2016 16:33:02 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: <569E572E.20203@uclouvain.be> Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit : > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% > sure I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users --- L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 14:02:45 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 14:02:45 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <569E572E.20203@uclouvain.be> References: <569E572E.20203@uclouvain.be> Message-ID: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > > ------------------------------ > [image: Avast logo] > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 20 03:33:47 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 20 Jan 2016 09:33:47 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > >> Hi, >> >> It looks like the geometry is wrong indeed, because I have never seen >> such artifacts. >> >> Hope that helps, >> Cyril >> >> >> Le 19/01/2016 16:19, MG Vallet a ?crit : >> >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data set from >> https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has been scanned. >> >> Attached is a view of the reconstructed central slice. It is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the proper term) >> >> My question is if these are simply expected artifacts. I am not 100% >> sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> >> ------------------------------ >> [image: Avast logo] >> >> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >> logiciel antivirus Avast. >> www.avast.com >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkfdk.sh Type: application/x-sh Size: 404 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: snapshot.jpg Type: image/jpeg Size: 95222 bytes Desc: not available URL: From mgvallet.pro at gmail.com Thu Jan 21 14:02:28 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 21 Jan 2016 14:02:28 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was SophiaBeads_512_averaged. Regarding the pre-processing mentioned by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > >> Thanks Cyril! >> going to carefully check my inputs and I give you some news. >> mgv >> >> 2016-01-19 10:33 GMT-05:00 Cyril Mory : >> >>> Hi, >>> >>> It looks like the geometry is wrong indeed, because I have never seen >>> such artifacts. >>> >>> Hope that helps, >>> Cyril >>> >>> >>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>> >>> Dear rtk-users, >>> >>> I applied the FDKConeBeamReconstructionFilter to a data set from >>> https://zenodo.org/record/16539. >>> This is a plastic tube filled with glass beads that has been scanned. >>> >>> Attached is a view of the reconstructed central slice. It is found that: >>> >>> 1. the beads are quickly deformed outside the center >>> 2. each one has a halo, or a shadow (dont know the proper term) >>> >>> My question is if these are simply expected artifacts. I am not 100% >>> sure I properly set the geometry parameters. >>> >>> Regards, >>> mgv >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >>> >>> ------------------------------ >>> [image: Avast logo] >>> >>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>> logiciel antivirus Avast. >>> www.avast.com >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_offset.jpg Type: image/jpeg Size: 52844 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Thu Jan 21 14:22:55 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Jan 2016 20:22:55 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: <56A1300F.1090509@creatis.insa-lyon.fr> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center > must effectively be offset (4.8 mm in both directions). For the > attached image, I also increases sdd and sid by a factor 1000, just in > case I would be wrong in units. It reduces the first default I pointed > out in my first message. Also note that my input dataset was > SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is > it as simple as the FDK filter assumes that the input is intensity, > but the dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit >: > > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems > that what is provided is directly the line integral. RTK will > process the tif images as if it were a photon count so I converted > the tif projections to mha to avoid this. For the conversion, I > used another piece of software but you can easily do the same > thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better > result. I have however a geometry problem. I think they provide a > Matlab piece of code to get the center of rotation. If you can run > it and find out what is this center, then you can use it to > configure the geometry better with the options --proj_iso_x and > --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet > wrote: > > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory >: > > Hi, > > It looks like the geometry is wrong indeed, because I have > never seen such artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data >> set from https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has >> been scanned. >> >> Attached is a view of the reconstructed central slice. It >> is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the >> proper term) >> >> My question is if these are simply expected artifacts. I >> am not 100% sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> >> http://public.kitware.com/mailman/listinfo/rtk-users > > > > ------------------------------------------------------------------------ > Avast logo > > L'absence de virus dans ce courrier ?lectronique a ?t? > v?rifi?e par le logiciel antivirus Avast. > www.avast.com > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 25 11:48:35 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 25 Jan 2016 11:48:35 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <56A1300F.1090509@creatis.insa-lyon.fr> References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > >> Hi, >> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >> is provided is directly the line integral. RTK will process the tif images >> as if it were a photon count so I converted the tif projections to mha to >> avoid this. For the conversion, I used another piece of software but you >> can easily do the same thing with SimpleRTK. >> Second, I used the enclosed script which gives me a much better result. I >> have however a geometry problem. I think they provide a Matlab piece of >> code to get the center of rotation. If you can run it and find out what is >> this center, then you can use it to configure the geometry better with the >> options --proj_iso_x and --proj_iso_y. >> Good luck, >> Simon >> >> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >> mgvallet.pro at gmail.com> wrote: >> >>> Thanks Cyril! >>> going to carefully check my inputs and I give you some news. >>> mgv >>> >>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>> cyril.mory at uclouvain.be>: >>> >>>> Hi, >>>> >>>> It looks like the geometry is wrong indeed, because I have never seen >>>> such artifacts. >>>> >>>> Hope that helps, >>>> Cyril >>>> >>>> >>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>> >>>> Dear rtk-users, >>>> >>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>> https://zenodo.org/record/16539. >>>> This is a plastic tube filled with glass beads that has been scanned. >>>> >>>> Attached is a view of the reconstructed central slice. It is found that: >>>> >>>> 1. the beads are quickly deformed outside the center >>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>> >>>> My question is if these are simply expected artifacts. I am not 100% >>>> sure I properly set the geometry parameters. >>>> >>>> Regards, >>>> mgv >>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> [image: Avast logo] >>>> >>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>> logiciel antivirus Avast. >>>> www.avast.com >>>> >>>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_log.jpg Type: image/jpeg Size: 17331 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 26 07:23:58 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Jan 2016 13:23:58 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > Hi Simon, > > this was a point I missed. I had to do the log mapping. > > I must say, I do not use RTK from shell. I just plugged the objects > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > MG > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > >> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the >> line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the >> projections and converts them depending on the type: for mha or mhd, it >> just reads it and nothing else. For tif, it assumes that I is passed, try >> to guess I0 (or gets it from the cmd line) and computes ln(I0/I). >> So from each tif projection, instead of letting them go through the >> ProjectionsReader in RTK, directly use the ImageReader, stack them and pass >> it to the reconstruction algorithm. In other words, if you use SimpleRTK, >> use ImageSeriesReader instead of ProjectionsReader. >> Regarding the geometry, it would be nice to be confident in the geometry >> parameters, maybe from their Matlab code? >> Simon >> >> >> On 21/01/2016 20:02, MG Vallet wrote: >> >> Hi Simon and Cyril, >> >> I really appreciate your insight. >> >> By examining the parameters of the acquisition, I saw that the center >> must effectively be offset (4.8 mm in both directions). For the attached >> image, I also increases sdd and sid by a factor 1000, just in case I would >> be wrong in units. It reduces the first default I pointed out in my first >> message. Also note that my input dataset was SophiaBeads_512_averaged. >> >> Regarding the pre-processing mentioned by Simon, I need more help. Is it >> as simple as the FDK filter assumes that the input is intensity, but the >> dataset provides -ln(I/I0) ? >> >> Regards, >> mg >> >> 2016-01-20 3:33 GMT-05:00 Simon Rit : >> >>> Hi, >>> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >>> is provided is directly the line integral. RTK will process the tif images >>> as if it were a photon count so I converted the tif projections to mha to >>> avoid this. For the conversion, I used another piece of software but you >>> can easily do the same thing with SimpleRTK. >>> Second, I used the enclosed script which gives me a much better result. >>> I have however a geometry problem. I think they provide a Matlab piece of >>> code to get the center of rotation. If you can run it and find out what is >>> this center, then you can use it to configure the geometry better with the >>> options --proj_iso_x and --proj_iso_y. >>> Good luck, >>> Simon >>> >>> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >>> mgvallet.pro at gmail.com> wrote: >>> >>>> Thanks Cyril! >>>> going to carefully check my inputs and I give you some news. >>>> mgv >>>> >>>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>>> cyril.mory at uclouvain.be>: >>>> >>>>> Hi, >>>>> >>>>> It looks like the geometry is wrong indeed, because I have never seen >>>>> such artifacts. >>>>> >>>>> Hope that helps, >>>>> Cyril >>>>> >>>>> >>>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>>> >>>>> Dear rtk-users, >>>>> >>>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>>> https://zenodo.org/record/16539. >>>>> This is a plastic tube filled with glass beads that has been scanned. >>>>> >>>>> Attached is a view of the reconstructed central slice. It is found >>>>> that: >>>>> >>>>> 1. the beads are quickly deformed outside the center >>>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>>> >>>>> My question is if these are simply expected artifacts. I am not 100% >>>>> sure I properly set the geometry parameters. >>>>> >>>>> Regards, >>>>> mgv >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> [image: Avast logo] >>>>> >>>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>>> logiciel antivirus Avast. >>>>> www.avast.com >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Jan 26 17:17:01 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 26 Jan 2016 23:17:01 +0100 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Hi MG, Sometimes, the progressive deformation from the center of rotation to the edge of the image is caused by wrong sdd/sid ratio. Such as change in the geometry will lead to distortion of the image and wrong magnification. Maybe you can play with that parameter and report your result. Cheers, Louie Sent from Mail for Windows 10 From: Simon Rit Sent: Tuesday, January 26, 2016 13:24 To: MG Vallet Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Sophia beads reconstruction Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and?ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was?SophiaBeads_512_averaged. Regarding the pre-processing?mentioned?by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit?: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from?https://zenodo.org/record/16539.? This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts.?I am not 100% sure I properly set the geometry parameters. Regards, mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. www.avast.com _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Thu Jan 28 16:27:15 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 28 Jan 2016 16:27:15 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: Louie, I played with sdd and sid, following your advise. But they have few effect, clearly less effect than proj_iso_x. And none of these parameters can significantly improve my result. Simon, I carefully checked every input data and I cant see what I did wrong. I want first to reproduce your output. You said earlier it's easy to convert a series of tiff image into a mha file using SimpleRTK. Do you mean by writing a short program, or is it possible from the command line ? MG 2016-01-26 17:17 GMT-05:00 louie L : > Hi MG, > > > > Sometimes, the progressive deformation from the center of rotation to the > edge of the image is caused by wrong sdd/sid ratio. Such as change in the > geometry will lead to distortion of the image and wrong magnification. > > Maybe you can play with that parameter and report your result. > > > > Cheers, > > Louie > > > > Sent from Mail for > Windows 10 > > > > > *From: *Simon Rit > *Sent: *Tuesday, January 26, 2016 13:24 > *To: *MG Vallet > *Cc: *rtk-users at public.kitware.com > *Subject: *Re: [Rtk-users] Sophia beads reconstruction > > > > Hi, > > I think it's likely a problem with parameters. The best would be to obtain > them from the Matlab code they provide. > > Good luck, > > Simon > > > > On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > > Hi Simon, > > > > this was a point I missed. I had to do the log mapping. > > > > I must say, I do not use RTK from shell. I just plugged the objects > > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > > > MG > > > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > > > I really appreciate your insight. > > > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > > > Regards, > > mg > > > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > > Hi, > > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > > Good luck, > > Simon > > > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > > Thanks Cyril! > > going to carefully check my inputs and I give you some news. > > mgv > > > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > > This is a plastic tube filled with glass beads that has been scanned. > > > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > > > Regards, > > mgv > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 4 16:55:56 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 4 Jan 2016 16:55:56 -0500 Subject: [Rtk-users] feldkamp application Message-ID: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Tue Jan 5 03:25:50 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 05 Jan 2016 09:25:50 +0100 Subject: [Rtk-users] feldkamp application In-Reply-To: References: Message-ID: <568B7E0E.9030904@uclouvain.be> Hi, and happy new year :) You can use the dataset provided for the motion-compensated reconstruction : http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Hope it helps, Cyril On 01/04/2016 10:55 PM, MG Vallet wrote: > Happy new year! > > Does someone have a data set, other than quadric phantoms, to test the > fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 5 05:16:50 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 5 Jan 2016 11:16:50 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: Message-ID: <568B9812.40404@creatis.insa-lyon.fr> Hi, I forgot to cc this email to the mailing list, in answers to mgv. Simon -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit To: MG Vallet Hi, There are vendor-specific examples available on the wiki: http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction You also have real patient data for 4D CBCT, e.g. http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction Simon On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: Happy new year! Does someone have a data set, other than quadric phantoms, to test the fdk module ? It would be fine to add one to the wiki page http://wiki.openrtk.org/index.php/Main_Page#Applications mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 5 16:50:09 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 5 Jan 2016 16:50:09 -0500 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: <568B9812.40404@creatis.insa-lyon.fr> References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: Thanks, Cyril and Simon. These applications seemed complicated to me, but it's only data reading that is. By the way, the command rtkfieldofview had no effect in the varian case (no error message, nor output file). Otherwise, everything's OK. 2016-01-05 5:16 GMT-05:00 Simon Rit : > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- Subject: Re: [Rtk-users] feldkamp > application Date: Tue, 5 Jan 2016 08:40:00 +0100 From: Simon Rit > To: MG > Vallet > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet wrote: > >> Happy new year! >> >> Does someone have a data set, other than quadric phantoms, to test the >> fdk module ? >> It would be fine to add one to the wiki page >> http://wiki.openrtk.org/index.php/Main_Page#Applications >> >> mgv >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Mon Jan 11 09:34:58 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Mon, 11 Jan 2016 15:34:58 +0100 Subject: [Rtk-users] Parker weighting In-Reply-To: <56743FCB.3040102@creatis.insa-lyon.fr> References: <56667F38.6040604@creatis.insa-lyon.fr> <56743FCB.3040102@creatis.insa-lyon.fr> Message-ID: Dear Simon, I am sorry for the late reply. I also wish you a happy new year. I will recheck if there is any error during generating projection images. The projections are generated from a volume with our simulation tool. However, I generated projections from the volume with rtkforwardprojections and I re-reconstructed the volume with rtkfdk. I did not get any artifacts. I will contact you soon, if I have some results. Thank you very much for your help. Shiras On Fri, Dec 18, 2015 at 6:18 PM, Simon Rit wrote: > Hi Shiras, > Sorry for the delayed answer, times are busy. The way RTK computes the > spanned arc is from the second projection angle to the before last > projection angle, i.e., in your case > 209.609216488925-11.6067737022482 > so it's a span of 199 degrees and your cone angle is indeed too large. > Like I said, this part of RTK is perfectible and there is no way to change > this but change the code. > However, the source of artefacts might be something else. On simulated > data, I tried: > rtkprojectshepploganphantom --like original_proj.mhd -g > geometry_parker_corr.xml -o proj.mha > rtkfdk -p . -r proj.mha -o fdk.mha -g geometry_parker_corr.xml > and the result is not that bad. What do you think? Can you show us a > snapshot if sg's wrong in your opinion? > Simon > > > On 09/12/2015 11:01, Shiras Abdurahman wrote: > > Dear Simon, > > I am attaching the mhd files of projections. > > With regards, > Shiras > > On Tue, Dec 8, 2015 at 6:17 PM, Simon Rit > wrote: > >> Hi, >> The geometry files look ok to me. What is the projection information? If >> you're still getting the same message as before, I think it's because you >> don't have enough data. If you send the mhd file of the projections (just >> the mhd, not the raw data), I can try to test it on simulated data to let >> you know my feeling. >> Simon >> >> On Tue, Dec 8, 2015 at 5:41 PM, Shiras Abdurahman < >> shiraska at gmail.com> wrote: >> >>> Dear Simon, >>> >>> I tried this option and unfortunately it did not work. I added zero >>> projections and modified geometry files. However, I am getting same >>> artifacts in the volume. Voxel values changed a little bit that indicates >>> during backprojection it still considers extreme projections. I am also >>> getting an output message same as before. >>> >>> I am attaching geometry files. >>> >>> With regards, >>> Shiras >>> >>> On Tue, Dec 8, 2015 at 10:15 AM, Simon Rit < >>> simon.rit at creatis.insa-lyon.fr> wrote: >>> >>>> So calling AddProjection before and after the loop with an adequate >>>> gantry_angle should work. >>>> Simon >>>> >>>> On Tue, Dec 8, 2015 at 9:52 AM, Shiras Abdurahman < >>>> shiraska at gmail.com> wrote: >>>> >>>>> Drear Simon, >>>>> >>>>> I generate the geometry with system geometry parameters and using >>>>> AddProjection method. >>>>> >>>>> Here is the code >>>>> >>>>> >>>>> rtk::ThreeDCircularProjectionGeometry::Pointer rtk_sys_geometry_; >>>>> rtk_sys_geometry_ = rtk::ThreeDCircularProjectionGeometry::New(); >>>>> for (uint16_t proj_index = 0; proj_index < num_projections_; >>>>> proj_index++) >>>>> { >>>>> >>>>> rtk_sys_geometry_->AddProjection(rtk_geom_params_.at(proj_index).sid_mm, >>>>> rtk_geom_params_.at(proj_index).sdd_mm, >>>>> rtk_geom_params_.at(proj_index).gantry_angle_deg, >>>>> rtk_geom_params_.at(proj_index).proj_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).proj_offset_y_mm, >>>>> rtk_geom_params_.at(proj_index).out_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).in_plane_angle_deg, >>>>> rtk_geom_params_.at(proj_index).src_offset_x_mm, >>>>> rtk_geom_params_.at(proj_index).src_offset_y_mm); >>>>> } >>>>> >>>>> And then write to xml file. >>>>> >>>>> Shiras >>>>> >>>>> >>>>> >>>>> On Tue, Dec 8, 2015 at 9:23 AM, Simon Rit < >>>>> simon.rit at creatis.insa-lyon.fr> wrote: >>>>> >>>>>> Hi, >>>>>> rtkfdk.cxx just read the geometry from a file so the best is to >>>>>> modify the geometry file. How do you generate the geometry? >>>>>> For example, if you use rtksimulated geometry, let's say that you >>>>>> were using: >>>>>> rtksimulatedgeometry -n 200 -a 200 -o g.xml >>>>>> then you'll have to replace it with >>>>>> rtksimulatedgeometry -n 202 -a 202 -o g.xml -f -1 >>>>>> Don't forget to add dummy projection at the beginning and the end. If >>>>>> you use a more complex geometry, maybe SimpleRTK >>>>>> can be helpful >>>>>> (I'd use that) or you'd have to modify the cxx code to add these additional >>>>>> projections in the geometry and the projection stack. >>>>>> Simon >>>>>> >>>>>> >>>>>> On Tue, Dec 8, 2015 at 8:51 AM, Shiras Abdurahman < >>>>>> shiraska at gmail.com> wrote: >>>>>> >>>>>>> Dear Simon, >>>>>>> >>>>>>> Thanks a lot for the reply. Can you please inform me how can I set >>>>>>> where the arc starts? >>>>>>> Do I need to modify geometry also? >>>>>>> If you can point the line of code rtkfdk.cxx, it will be really >>>>>>> helpful. >>>>>>> >>>>>>> With regards, >>>>>>> Shiras >>>>>>> >>>>>>> On Tue, Dec 8, 2015 at 7:56 AM, Simon Rit < >>>>>>> simon.rit at creatis.insa-lyon.fr> >>>>>>> wrote: >>>>>>> >>>>>>>> Dear Shiras, >>>>>>>> Yes, for practical reasons the first and the last projections are >>>>>>>> set to 0 and the arc used in the Parker weighting starts between the first >>>>>>>> two projections and ends between the lasts two projections. There is a >>>>>>>> simple solution: add a projection at the beginning and the end of the arc, >>>>>>>> which can contain any pixel values but should be set where you want this >>>>>>>> arc to start. In the future, I think someone should once take the time to >>>>>>>> correct this but I haven't so far. I'll keep you posted on the mailing list >>>>>>>> when it's corrected. >>>>>>>> Simon >>>>>>>> >>>>>>>> On 07/12/2015 12:04, Shiras Abdurahman wrote: >>>>>>>> >>>>>>>> Hi all, >>>>>>>> >>>>>>>> I am trying to reconstruct a volume from projection data generated >>>>>>>> with C-arm CT. There are 248 projections with an angular range of 199 >>>>>>>> degree. Technically, parker weighting should run without any problems. >>>>>>>> However, I am getting an output message that "You do not have enough data >>>>>>>> for proper parker weighting". After parker weighting, the two extreme >>>>>>>> projections (projection number 1 and 248) were completely zero and thus >>>>>>>> reconstructed volume contained artifacts. When I increased the angular >>>>>>>> range, this problem did not happen. How can I solve this problem without >>>>>>>> increasing angular range? Is there any threshold constant that I can change >>>>>>>> in command line or in my code? >>>>>>>> >>>>>>>> I really appreciate any help you can provide. >>>>>>>> >>>>>>>> With regards, >>>>>>>> Shiras >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 12 07:47:46 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 12 Jan 2016 13:47:46 +0100 Subject: [Rtk-users] Fwd: Re: feldkamp application In-Reply-To: References: <568B9812.40404@creatis.insa-lyon.fr> Message-ID: <5694F5F2.4060702@creatis.insa-lyon.fr> Hi, There was a typo on the folder path (../Scan0 instead of Scan0). Was that the problem? I checked and it has the expected effect, i.e., setting to 0 everything outside the FOV. Simon On 05/01/2016 22:50, MG Vallet wrote: > Thanks, Cyril and Simon. > These applications seemed complicated to me, but it's only data > reading that is. > By the way, the command rtkfieldofview had no effect in the varian > case (no error message, nor output file). Otherwise, everything's OK. > > 2016-01-05 5:16 GMT-05:00 Simon Rit >: > > Hi, > I forgot to cc this email to the mailing list, in answers to mgv. > Simon > > > > -------- Forwarded Message -------- > Subject: Re: [Rtk-users] feldkamp application > Date: Tue, 5 Jan 2016 08:40:00 +0100 > From: Simon Rit > > To: MG Vallet > > > > > Hi, > There are vendor-specific examples available on the wiki: > http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > You also have real patient data for 4D CBCT, e.g. > http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction > Simon > > > On Mon, Jan 4, 2016 at 10:55 PM, MG Vallet > wrote: > > Happy new year! > > Does someone have a data set, other than quadric phantoms, to > test the fdk module ? > It would be fine to add one to the wiki page > http://wiki.openrtk.org/index.php/Main_Page#Applications > > mgv > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shiraska at gmail.com Wed Jan 13 07:42:45 2016 From: shiraska at gmail.com (Shiras Abdurahman) Date: Wed, 13 Jan 2016 13:42:45 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry Message-ID: Dear all, I am trying to generate geometry xml file with rtkReg23ProjectionGeometry after decomposing projection matrix. One of the argument to the function AddReg23Projection is detector position. I assume that, it is the position vector of the center of the first pixel in world co-ordinates. This will be used for computing the projection offset parameters by projecting detector origin vector onto the u and v axis of the detector. If that is the case, do we need to change the offset parameters of each projection in the mhd file. Will this create problems during displaced detector correction? With regards, Shiras -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 13 13:31:23 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Jan 2016 19:31:23 +0100 Subject: [Rtk-users] rtkReg23ProjectionGeometry In-Reply-To: References: Message-ID: <569697FB.1020804@creatis.insa-lyon.fr> Hi, Wrong assumption. It's the coordinate of point (0,0) in the coordinate of the projection image in the word coordinates, it's not the coordinate of the center of the first pixel. This is mentioned in the geometry description file on the wiki. You should not change the mhd parameters. If you want to account for offset parameters that change from projection to projection, you can put that offset in the computation of the detector position in world coordinates. Simon On 13/01/2016 13:42, Shiras Abdurahman wrote: > Dear all, > > I am trying to generate geometry xml file with > rtkReg23ProjectionGeometry after decomposing projection matrix. One of > the argument to the function AddReg23Projection is detector position. > I assume that, it is the position vector of the center of the first > pixel in world co-ordinates. This will be used for computing the > projection offset parameters by projecting detector origin vector onto > the u and v axis of the detector. If that is the case, do we need to > change the offset parameters of each projection in the mhd file. Will > this create problems during displaced detector correction? > > > With regards, > Shiras > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 10:19:12 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 10:19:12 -0500 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from https://zenodo.org/record/16539. This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts. I am not 100% sure I properly set the geometry parameters. Regards, mgv -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sophiaBeadsCentralSlide.jpg Type: image/jpeg Size: 55394 bytes Desc: not available URL: From cyril.mory at uclouvain.be Tue Jan 19 10:33:02 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Tue, 19 Jan 2016 16:33:02 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: <569E572E.20203@uclouvain.be> Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit : > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% > sure I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users --- L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Tue Jan 19 14:02:45 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Tue, 19 Jan 2016 14:02:45 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <569E572E.20203@uclouvain.be> References: <569E572E.20203@uclouvain.be> Message-ID: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > This is a plastic tube filled with glass beads that has been scanned. > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > Regards, > mgv > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > > ------------------------------ > [image: Avast logo] > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Jan 20 03:33:47 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 20 Jan 2016 09:33:47 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > >> Hi, >> >> It looks like the geometry is wrong indeed, because I have never seen >> such artifacts. >> >> Hope that helps, >> Cyril >> >> >> Le 19/01/2016 16:19, MG Vallet a ?crit : >> >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data set from >> https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has been scanned. >> >> Attached is a view of the reconstructed central slice. It is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the proper term) >> >> My question is if these are simply expected artifacts. I am not 100% >> sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> >> ------------------------------ >> [image: Avast logo] >> >> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >> logiciel antivirus Avast. >> www.avast.com >> >> > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rtkfdk.sh Type: application/x-sh Size: 404 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: snapshot.jpg Type: image/jpeg Size: 95222 bytes Desc: not available URL: From mgvallet.pro at gmail.com Thu Jan 21 14:02:28 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 21 Jan 2016 14:02:28 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was SophiaBeads_512_averaged. Regarding the pre-processing mentioned by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > >> Thanks Cyril! >> going to carefully check my inputs and I give you some news. >> mgv >> >> 2016-01-19 10:33 GMT-05:00 Cyril Mory : >> >>> Hi, >>> >>> It looks like the geometry is wrong indeed, because I have never seen >>> such artifacts. >>> >>> Hope that helps, >>> Cyril >>> >>> >>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>> >>> Dear rtk-users, >>> >>> I applied the FDKConeBeamReconstructionFilter to a data set from >>> https://zenodo.org/record/16539. >>> This is a plastic tube filled with glass beads that has been scanned. >>> >>> Attached is a view of the reconstructed central slice. It is found that: >>> >>> 1. the beads are quickly deformed outside the center >>> 2. each one has a halo, or a shadow (dont know the proper term) >>> >>> My question is if these are simply expected artifacts. I am not 100% >>> sure I properly set the geometry parameters. >>> >>> Regards, >>> mgv >>> >>> >>> _______________________________________________ >>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >>> >>> >>> ------------------------------ >>> [image: Avast logo] >>> >>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>> logiciel antivirus Avast. >>> www.avast.com >>> >>> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_offset.jpg Type: image/jpeg Size: 52844 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Thu Jan 21 14:22:55 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 21 Jan 2016 20:22:55 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> Message-ID: <56A1300F.1090509@creatis.insa-lyon.fr> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center > must effectively be offset (4.8 mm in both directions). For the > attached image, I also increases sdd and sid by a factor 1000, just in > case I would be wrong in units. It reduces the first default I pointed > out in my first message. Also note that my input dataset was > SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is > it as simple as the FDK filter assumes that the input is intensity, > but the dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit >: > > Hi, > I quickly checked SophiaBeads_64_averaged.zip. First, it seems > that what is provided is directly the line integral. RTK will > process the tif images as if it were a photon count so I converted > the tif projections to mha to avoid this. For the conversion, I > used another piece of software but you can easily do the same > thing with SimpleRTK. > Second, I used the enclosed script which gives me a much better > result. I have however a geometry problem. I think they provide a > Matlab piece of code to get the center of rotation. If you can run > it and find out what is this center, then you can use it to > configure the geometry better with the options --proj_iso_x and > --proj_iso_y. > Good luck, > Simon > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet > wrote: > > Thanks Cyril! > going to carefully check my inputs and I give you some news. > mgv > > 2016-01-19 10:33 GMT-05:00 Cyril Mory >: > > Hi, > > It looks like the geometry is wrong indeed, because I have > never seen such artifacts. > > Hope that helps, > Cyril > > > Le 19/01/2016 16:19, MG Vallet a ?crit : >> Dear rtk-users, >> >> I applied the FDKConeBeamReconstructionFilter to a data >> set from https://zenodo.org/record/16539. >> This is a plastic tube filled with glass beads that has >> been scanned. >> >> Attached is a view of the reconstructed central slice. It >> is found that: >> >> 1. the beads are quickly deformed outside the center >> 2. each one has a halo, or a shadow (dont know the >> proper term) >> >> My question is if these are simply expected artifacts. I >> am not 100% sure I properly set the geometry parameters. >> >> Regards, >> mgv >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> >> http://public.kitware.com/mailman/listinfo/rtk-users > > > > ------------------------------------------------------------------------ > Avast logo > > L'absence de virus dans ce courrier ?lectronique a ?t? > v?rifi?e par le logiciel antivirus Avast. > www.avast.com > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Mon Jan 25 11:48:35 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Mon, 25 Jan 2016 11:48:35 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: <56A1300F.1090509@creatis.insa-lyon.fr> References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > I really appreciate your insight. > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > Regards, > mg > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > >> Hi, >> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >> is provided is directly the line integral. RTK will process the tif images >> as if it were a photon count so I converted the tif projections to mha to >> avoid this. For the conversion, I used another piece of software but you >> can easily do the same thing with SimpleRTK. >> Second, I used the enclosed script which gives me a much better result. I >> have however a geometry problem. I think they provide a Matlab piece of >> code to get the center of rotation. If you can run it and find out what is >> this center, then you can use it to configure the geometry better with the >> options --proj_iso_x and --proj_iso_y. >> Good luck, >> Simon >> >> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >> mgvallet.pro at gmail.com> wrote: >> >>> Thanks Cyril! >>> going to carefully check my inputs and I give you some news. >>> mgv >>> >>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>> cyril.mory at uclouvain.be>: >>> >>>> Hi, >>>> >>>> It looks like the geometry is wrong indeed, because I have never seen >>>> such artifacts. >>>> >>>> Hope that helps, >>>> Cyril >>>> >>>> >>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>> >>>> Dear rtk-users, >>>> >>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>> https://zenodo.org/record/16539. >>>> This is a plastic tube filled with glass beads that has been scanned. >>>> >>>> Attached is a view of the reconstructed central slice. It is found that: >>>> >>>> 1. the beads are quickly deformed outside the center >>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>> >>>> My question is if these are simply expected artifacts. I am not 100% >>>> sure I properly set the geometry parameters. >>>> >>>> Regards, >>>> mgv >>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> [image: Avast logo] >>>> >>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>> logiciel antivirus Avast. >>>> www.avast.com >>>> >>>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: slice0_log.jpg Type: image/jpeg Size: 17331 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Tue Jan 26 07:23:58 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Jan 2016 13:23:58 +0100 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: <569E572E.20203@uclouvain.be> <56A1300F.1090509@creatis.insa-lyon.fr> Message-ID: Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > Hi Simon, > > this was a point I missed. I had to do the log mapping. > > I must say, I do not use RTK from shell. I just plugged the objects > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > MG > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > >> Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the >> line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the >> projections and converts them depending on the type: for mha or mhd, it >> just reads it and nothing else. For tif, it assumes that I is passed, try >> to guess I0 (or gets it from the cmd line) and computes ln(I0/I). >> So from each tif projection, instead of letting them go through the >> ProjectionsReader in RTK, directly use the ImageReader, stack them and pass >> it to the reconstruction algorithm. In other words, if you use SimpleRTK, >> use ImageSeriesReader instead of ProjectionsReader. >> Regarding the geometry, it would be nice to be confident in the geometry >> parameters, maybe from their Matlab code? >> Simon >> >> >> On 21/01/2016 20:02, MG Vallet wrote: >> >> Hi Simon and Cyril, >> >> I really appreciate your insight. >> >> By examining the parameters of the acquisition, I saw that the center >> must effectively be offset (4.8 mm in both directions). For the attached >> image, I also increases sdd and sid by a factor 1000, just in case I would >> be wrong in units. It reduces the first default I pointed out in my first >> message. Also note that my input dataset was SophiaBeads_512_averaged. >> >> Regarding the pre-processing mentioned by Simon, I need more help. Is it >> as simple as the FDK filter assumes that the input is intensity, but the >> dataset provides -ln(I/I0) ? >> >> Regards, >> mg >> >> 2016-01-20 3:33 GMT-05:00 Simon Rit : >> >>> Hi, >>> I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what >>> is provided is directly the line integral. RTK will process the tif images >>> as if it were a photon count so I converted the tif projections to mha to >>> avoid this. For the conversion, I used another piece of software but you >>> can easily do the same thing with SimpleRTK. >>> Second, I used the enclosed script which gives me a much better result. >>> I have however a geometry problem. I think they provide a Matlab piece of >>> code to get the center of rotation. If you can run it and find out what is >>> this center, then you can use it to configure the geometry better with the >>> options --proj_iso_x and --proj_iso_y. >>> Good luck, >>> Simon >>> >>> On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet < >>> mgvallet.pro at gmail.com> wrote: >>> >>>> Thanks Cyril! >>>> going to carefully check my inputs and I give you some news. >>>> mgv >>>> >>>> 2016-01-19 10:33 GMT-05:00 Cyril Mory < >>>> cyril.mory at uclouvain.be>: >>>> >>>>> Hi, >>>>> >>>>> It looks like the geometry is wrong indeed, because I have never seen >>>>> such artifacts. >>>>> >>>>> Hope that helps, >>>>> Cyril >>>>> >>>>> >>>>> Le 19/01/2016 16:19, MG Vallet a ?crit : >>>>> >>>>> Dear rtk-users, >>>>> >>>>> I applied the FDKConeBeamReconstructionFilter to a data set from >>>>> https://zenodo.org/record/16539. >>>>> This is a plastic tube filled with glass beads that has been scanned. >>>>> >>>>> Attached is a view of the reconstructed central slice. It is found >>>>> that: >>>>> >>>>> 1. the beads are quickly deformed outside the center >>>>> 2. each one has a halo, or a shadow (dont know the proper term) >>>>> >>>>> My question is if these are simply expected artifacts. I am not 100% >>>>> sure I properly set the geometry parameters. >>>>> >>>>> Regards, >>>>> mgv >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> [image: Avast logo] >>>>> >>>>> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le >>>>> logiciel antivirus Avast. >>>>> www.avast.com >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Rtk-users mailing list >>>> Rtk-users at public.kitware.com >>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>> >>>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Tue Jan 26 17:17:01 2016 From: ghostcz at hotmail.com (louie L) Date: Tue, 26 Jan 2016 23:17:01 +0100 Subject: [Rtk-users] Sophia beads reconstruction Message-ID: Hi MG, Sometimes, the progressive deformation from the center of rotation to the edge of the image is caused by wrong sdd/sid ratio. Such as change in the geometry will lead to distortion of the image and wrong magnification. Maybe you can play with that parameter and report your result. Cheers, Louie Sent from Mail for Windows 10 From: Simon Rit Sent: Tuesday, January 26, 2016 13:24 To: MG Vallet Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Sophia beads reconstruction Hi, I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide. Good luck, Simon On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: Hi Simon, this was a point I missed. I had to do the log mapping. I must say, I do not use RTK from shell. I just plugged the objects FDKConeBeamReconstructionFilter and?ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting. Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center. What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ? MG 2016-01-21 14:22 GMT-05:00 Simon Rit : Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I). So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader. Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code? Simon On 21/01/2016 20:02, MG Vallet wrote: Hi Simon and Cyril, I really appreciate your insight. By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was?SophiaBeads_512_averaged. Regarding the pre-processing?mentioned?by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ? Regards, mg 2016-01-20 3:33 GMT-05:00 Simon Rit : Hi, I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK. Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y. Good luck, Simon On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: Thanks Cyril! going to carefully check my inputs and I give you some news. mgv 2016-01-19 10:33 GMT-05:00 Cyril Mory : Hi, It looks like the geometry is wrong indeed, because I have never seen such artifacts. Hope that helps, Cyril Le 19/01/2016 16:19, MG Vallet a ?crit?: Dear rtk-users, I applied the FDKConeBeamReconstructionFilter to a data set from?https://zenodo.org/record/16539.? This is a plastic tube filled with glass beads that has been scanned. Attached is a view of the reconstructed central slice. It is found that: 1. the beads are quickly deformed outside the center 2. each one has a halo, or a shadow (dont know the proper term) My question is if these are simply expected artifacts.?I am not 100% sure I properly set the geometry parameters. Regards, mgv _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. www.avast.com _______________________________________________ Rtk-users mailing list Rtk-users at public.kitware.com http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgvallet.pro at gmail.com Thu Jan 28 16:27:15 2016 From: mgvallet.pro at gmail.com (MG Vallet) Date: Thu, 28 Jan 2016 16:27:15 -0500 Subject: [Rtk-users] Sophia beads reconstruction In-Reply-To: References: Message-ID: Louie, I played with sdd and sid, following your advise. But they have few effect, clearly less effect than proj_iso_x. And none of these parameters can significantly improve my result. Simon, I carefully checked every input data and I cant see what I did wrong. I want first to reproduce your output. You said earlier it's easy to convert a series of tiff image into a mha file using SimpleRTK. Do you mean by writing a short program, or is it possible from the command line ? MG 2016-01-26 17:17 GMT-05:00 louie L : > Hi MG, > > > > Sometimes, the progressive deformation from the center of rotation to the > edge of the image is caused by wrong sdd/sid ratio. Such as change in the > geometry will lead to distortion of the image and wrong magnification. > > Maybe you can play with that parameter and report your result. > > > > Cheers, > > Louie > > > > Sent from Mail for > Windows 10 > > > > > *From: *Simon Rit > *Sent: *Tuesday, January 26, 2016 13:24 > *To: *MG Vallet > *Cc: *rtk-users at public.kitware.com > *Subject: *Re: [Rtk-users] Sophia beads reconstruction > > > > Hi, > > I think it's likely a problem with parameters. The best would be to obtain > them from the Matlab code they provide. > > Good luck, > > Simon > > > > On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet wrote: > > Hi Simon, > > > > this was a point I missed. I had to do the log mapping. > > > > I must say, I do not use RTK from shell. I just plugged the objects > > FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from > RTK into a visualisation software. That's the reason I'm not absolutely > sure about the length parameter setting. > > > > Anyway, I'm now pretty close to your result. I believe the only difference > is the progressive deformation of beads with the distance to center. > > > > What's your opinion : is there another step I might have missed, or is it > more likely a problem with parameters ? > > > > MG > > > > 2016-01-21 14:22 GMT-05:00 Simon Rit : > > Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the > line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the > projections and converts them depending on the type: for mha or mhd, it > just reads it and nothing else. For tif, it assumes that I is passed, try > to guess I0 (or gets it from the cmd line) and computes ln(I0/I). > So from each tif projection, instead of letting them go through the > ProjectionsReader in RTK, directly use the ImageReader, stack them and pass > it to the reconstruction algorithm. In other words, if you use SimpleRTK, > use ImageSeriesReader instead of ProjectionsReader. > Regarding the geometry, it would be nice to be confident in the geometry > parameters, maybe from their Matlab code? > Simon > > > > On 21/01/2016 20:02, MG Vallet wrote: > > Hi Simon and Cyril, > > > > I really appreciate your insight. > > > > By examining the parameters of the acquisition, I saw that the center must > effectively be offset (4.8 mm in both directions). For the attached image, > I also increases sdd and sid by a factor 1000, just in case I would be > wrong in units. It reduces the first default I pointed out in my first > message. Also note that my input dataset was SophiaBeads_512_averaged. > > > > Regarding the pre-processing mentioned by Simon, I need more help. Is it > as simple as the FDK filter assumes that the input is intensity, but the > dataset provides -ln(I/I0) ? > > > > Regards, > > mg > > > > 2016-01-20 3:33 GMT-05:00 Simon Rit : > > Hi, > > I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what > is provided is directly the line integral. RTK will process the tif images > as if it were a photon count so I converted the tif projections to mha to > avoid this. For the conversion, I used another piece of software but you > can easily do the same thing with SimpleRTK. > > Second, I used the enclosed script which gives me a much better result. I > have however a geometry problem. I think they provide a Matlab piece of > code to get the center of rotation. If you can run it and find out what is > this center, then you can use it to configure the geometry better with the > options --proj_iso_x and --proj_iso_y. > > Good luck, > > Simon > > > > On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet wrote: > > Thanks Cyril! > > going to carefully check my inputs and I give you some news. > > mgv > > > > 2016-01-19 10:33 GMT-05:00 Cyril Mory : > > Hi, > > It looks like the geometry is wrong indeed, because I have never seen such > artifacts. > > Hope that helps, > Cyril > > > > Le 19/01/2016 16:19, MG Vallet a ?crit : > > Dear rtk-users, > > > > I applied the FDKConeBeamReconstructionFilter to a data set from > https://zenodo.org/record/16539. > > This is a plastic tube filled with glass beads that has been scanned. > > > > Attached is a view of the reconstructed central slice. It is found that: > > 1. the beads are quickly deformed outside the center > 2. each one has a halo, or a shadow (dont know the proper term) > > My question is if these are simply expected artifacts. I am not 100% sure > I properly set the geometry parameters. > > > > Regards, > > mgv > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le > logiciel antivirus Avast. > www.avast.com > > > > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: