From simon.rit at creatis.insa-lyon.fr Thu May 4 15:07:55 2017 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 4 May 2017 21:07:55 +0200 Subject: [Rtk-users] SimpleRTK In-Reply-To: References: Message-ID: Dear Sareh, Please use the mailing list, there might be someone else that can answer. I don't know how to use Conrad data in RTK but I'd be interested. We can try to support if you explain the problem. If you find out how to do it, please let us know. Best regards, Simon On Thu, May 4, 2017 at 6:44 PM, sare Borhani wrote: > Dear Simon, > > During my work, I need to be able to take backward and forward > projections.For this reason, I had chosen RTK. > > But I need to work with different 3D phantoms. I got several phantoms using > Conrad. > Now my problem is how to use them in RTK for having RTK-3D volume and then > their 2D projections.I used the only example and already have one phantom > but I have no idea how I can use it again for other phantoms. > > I tried to get the answer from the testing.cxx but they all are written in > CPP. > > Please help me. > > Best regards, > Sareh From pascal.bourgault at gmail.com Thu May 4 15:34:49 2017 From: pascal.bourgault at gmail.com (Pascal Bourgault) Date: Thu, 4 May 2017 15:34:49 -0400 Subject: [Rtk-users] SimpleRTK In-Reply-To: References: Message-ID: @Sareh I'm not completely sure what your problem is, but for the forward- and back- projections without going through C++, you can use the : "rtkforwardprojections" and "rtkbackprojections" applications created when you compile the complete RTK folder. They both take a geometry file in input + a volume for the first or the projections for the second. Then you could do whatever you want with the intermediary results. I do not know Conrad and haven't achieved getting information about their phantoms. Could you give us more info about how the file format of those phantoms? -- Pascal 2017-05-04 15:07 GMT-04:00 Simon Rit : > Dear Sareh, > Please use the mailing list, there might be someone else that can answer. > I don't know how to use Conrad data in RTK but I'd be interested. We > can try to support if you explain the problem. If you find out how to > do it, please let us know. > Best regards, > Simon > > On Thu, May 4, 2017 at 6:44 PM, sare Borhani > wrote: > > Dear Simon, > > > > During my work, I need to be able to take backward and forward > > projections.For this reason, I had chosen RTK. > > > > But I need to work with different 3D phantoms. I got several phantoms > using > > Conrad. > > Now my problem is how to use them in RTK for having RTK-3D volume and > then > > their 2D projections.I used the only example and already have one phantom > > but I have no idea how I can use it again for other phantoms. > > > > I tried to get the answer from the testing.cxx but they all are written > in > > CPP. > > > > Please help me. > > > > Best regards, > > Sareh > _______________________________________________ > 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 jafs at force.dk Mon May 15 09:48:11 2017 From: jafs at force.dk (=?iso-8859-1?Q?Jacob_Fr=F8sig?=) Date: Mon, 15 May 2017 13:48:11 +0000 Subject: [Rtk-users] Reconstructing from fan-beam projections Message-ID: Dear Rtk-users I was wandering if Rtk includes an implementation of a reconstruction method to reconstruct a 2D representation of an object given fan-beam projections. Or, if anyone has experience using e.g. FDKConeBeamReconstructionFilter on projections from line-detectors (fan-beam instead of cone-beam). I hope you guys can help. Yours sincerely Jacob Fr?sig Project Manager Sensor Innovation FORCE Technology Park All? 345 2605 Br?ndby Denmark Phone: +45 43 25 00 00 Direct: +45 43 25 16 43 Skype for Business: jafs at forcetechnology.com Fax: +45 43 25 00 10 e-mail: jafs at force.dk www: forcetechnology.com ************************************************************************* This email and any files transmitted with it may contain confidential information intended for the addressee(s) only. The information is not to be surrendered or copied to unauthorised persons. If you have received this communication in error, please notify us immediately by email at: info at forcetechnology.com ************************************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From ghostcz at hotmail.com Mon May 15 10:01:15 2017 From: ghostcz at hotmail.com (louie L) Date: Mon, 15 May 2017 14:01:15 +0000 Subject: [Rtk-users] Reconstructing from fan-beam projections In-Reply-To: References: Message-ID: Hi, I think you can carefully pad zeros to your projections. Reconstruct as if it is a 3d object. Take the middle slice as your fanbeam result. Let me know if it helps. Best regards, Louie Sent from my iOS Am 15.05.2017 um 15:55 schrieb Jacob Fr?sig >: Dear Rtk-users I was wandering if Rtk includes an implementation of a reconstruction method to reconstruct a 2D representation of an object given fan-beam projections. Or, if anyone has experience using e.g. FDKConeBeamReconstructionFilter on projections from line-detectors (fan-beam instead of cone-beam). I hope you guys can help. Yours sincerely Jacob Fr?sig Project Manager Sensor Innovation FORCE Technology Park All? 345 2605 Br?ndby Denmark Phone: +45 43 25 00 00 Direct: +45 43 25 16 43 Skype for Business: jafs at forcetechnology.com Fax: +45 43 25 00 10 e-mail: jafs at force.dk www: forcetechnology.com ************************************************************************* This email and any files transmitted with it may contain confidential information intended for the addressee(s) only. The information is not to be surrendered or copied to unauthorised persons. If you have received this communication in error, please notify us immediately by email at: info at forcetechnology.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 simon.rit at creatis.insa-lyon.fr Mon May 15 10:04:48 2017 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 15 May 2017 16:04:48 +0200 Subject: [Rtk-users] Reconstructing from fan-beam projections In-Reply-To: References: Message-ID: Hi, I agree. What I do is do a 3 slice sinogram from the fan-beam projections by copying the same data in each slice but reconstruct one 2D slice. If you need an example, I can quickly demonstrate this in a short Python script. Simon On Mon, May 15, 2017 at 4:01 PM, louie L wrote: > Hi, > > I think you can carefully pad zeros to your projections. Reconstruct as if > it is a 3d object. Take the middle slice as your fanbeam result. > Let me know if it helps. > > Best regards, > Louie > > Sent from my iOS > > Am 15.05.2017 um 15:55 schrieb Jacob Fr?sig : > > Dear Rtk-users > > > > I was wandering if Rtk includes an implementation of a reconstruction > method to reconstruct a 2D representation of an object given fan-beam > projections. > > Or, if anyone has experience using e.g. FDKConeBeamReconstructionFilter > on projections from line-detectors (fan-beam instead of cone-beam). > > > > I hope you guys can help. > > Yours sincerely > > *Jacob Fr?sig * > > Project Manager > Sensor Innovation > > FORCE Technology > Park All? 345 > 2605 Br?ndby > Denmark > > Phone: +45 43 25 00 00 <+45%2043%2025%2000%2000> > Direct: +45 43 25 16 43 <+45%2043%2025%2016%2043> > Skype for Business: jafs at forcetechnology.com > Fax: +45 43 25 00 10 <+45%2043%2025%2000%2010> > e-mail: jafs at force.dk > www: forcetechnology.com > > > ************************************************************************* > This email and any files transmitted with it may contain confidential > information intended for the addressee(s) only. The information is not to > be > surrendered or copied to unauthorised persons. If you have received > this communication in error, please notify us immediately by email at: > info at forcetechnology.com > ************************************************************************* > > _______________________________________________ > 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 simon.rit at creatis.insa-lyon.fr Mon May 15 11:32:17 2017 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 15 May 2017 17:32:17 +0200 Subject: [Rtk-users] Reconstructing from fan-beam projections In-Reply-To: References: Message-ID: Hi, I have added an example here: http://wiki.openrtk.org/index.php/FanBeam The values in the first and the third rows are not used, as illustrated in this example. We add them to do a 2D interpolation but we do this 2D interpolation exactly on the second row so that's not a problem. Note that it's a bit more tricky for iterative recon but we also have a solution for this if you need it. Best regards, Simon On Mon, May 15, 2017 at 4:31 PM, Jacob Fr?sig wrote: > Hi again, > > > > Thank you for the quick answer! An example would be great, thanks. I have > one concern about copying the fan-beam data: > > > Then we would have 2D projections for which each column is the same > fan-beam projection. By this, values of the same row are equal even though > the cone-beam geometry indicates the outer columns correspond to > intensities of rays with longer travel time through the object and hence > should have attenuated more. Is this neglectable? > > > > Again, thanks! > > > > Best regards, > > Jacob > > > > > > > > *From:* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *On Behalf Of *Simon > Rit > *Sent:* 15. maj 2017 16:05 > *To:* louie L > *Cc:* Jacob Fr?sig ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi, > > I agree. What I do is do a 3 slice sinogram from the fan-beam projections > by copying the same data in each slice but reconstruct one 2D slice. If you > need an example, I can quickly demonstrate this in a short Python script. > > Simon > > > > On Mon, May 15, 2017 at 4:01 PM, louie L wrote: > > Hi, > > > > I think you can carefully pad zeros to your projections. Reconstruct as if > it is a 3d object. Take the middle slice as your fanbeam result. > > Let me know if it helps. > > > > Best regards, > > Louie > > Sent from my iOS > > > Am 15.05.2017 um 15:55 schrieb Jacob Fr?sig : > > Dear Rtk-users > > > > I was wandering if Rtk includes an implementation of a reconstruction > method to reconstruct a 2D representation of an object given fan-beam > projections. > > Or, if anyone has experience using e.g. FDKConeBeamReconstructionFilter > on projections from line-detectors (fan-beam instead of cone-beam). > > > > I hope you guys can help. > > Yours sincerely > > *Jacob Fr?sig * > > Project Manager > Sensor Innovation > > FORCE Technology > Park All? 345 > 2605 Br?ndby > Denmark > > Phone: +45 43 25 00 00 <+45%2043%2025%2000%2000> > Direct: +45 43 25 16 43 <+45%2043%2025%2016%2043> > Skype for Business: jafs at forcetechnology.com > Fax: +45 43 25 00 10 <+45%2043%2025%2000%2010> > e-mail: jafs at force.dk > www: forcetechnology.com > > > ************************************************************************* > This email and any files transmitted with it may contain confidential > information intended for the addressee(s) only. The information is not to > be > surrendered or copied to unauthorised persons. If you have received > this communication in error, please notify us immediately by email at: > info at forcetechnology.com > ************************************************************************* > > _______________________________________________ > 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 simon.rit at creatis.insa-lyon.fr Tue May 16 08:54:24 2017 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 16 May 2017 14:54:24 +0200 Subject: [Rtk-users] Reconstructing from fan-beam projections In-Reply-To: References: Message-ID: Hi Jacob, Thanks for the image of the sinogram. I don't understand this sinogram. Do you know how to convert each pixel value to a line integral? I.e., if it's x-ray imaging, do you have an image without object? Thanks, Simon On Tue, May 16, 2017 at 2:24 PM, Jacob Fr?sig wrote: > Hi again, > > and thank you for the example! > > I have some trouble getting a proper reconstruction. If you have the time, > any help would be appreciated. > > Attached is my fan-beam sinogram as a .tif file. Here, projections are > taken for 360 degrees and the detector has 507 pixels. > I believe the issue lies in setting the geometry and maybe the spacing > between the pixels. The measurement geometry is as follows > > Source to centre: 590 mm > > Source to detector: 1000 mm > > Detector length: 411mm > > > > Best regards, > > > > Jacob > > > > > > *From:* Rtk-users [mailto:rtk-users-bounces at public.kitware.com] *On > Behalf Of *Simon Rit > *Sent:* 15. maj 2017 17:32 > *To:* rtk-users at openrtk.org > > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi, > > I have added an example here: > http://wiki.openrtk.org/index.php/FanBeam > > The values in the first and the third rows are not used, as illustrated in > this example. We add them to do a 2D interpolation but we do this 2D > interpolation exactly on the second row so that's not a problem. > > Note that it's a bit more tricky for iterative recon but we also have a > solution for this if you need it. > > Best regards, > > Simon > > > > On Mon, May 15, 2017 at 4:31 PM, Jacob Fr?sig wrote: > > Hi again, > > > > Thank you for the quick answer! An example would be great, thanks. I have > one concern about copying the fan-beam data: > > > Then we would have 2D projections for which each column is the same > fan-beam projection. By this, values of the same row are equal even though > the cone-beam geometry indicates the outer columns correspond to > intensities of rays with longer travel time through the object and hence > should have attenuated more. Is this neglectable? > > > > Again, thanks! > > > > Best regards, > > Jacob > > > > > > > > *From:* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *On Behalf Of *Simon > Rit > *Sent:* 15. maj 2017 16:05 > *To:* louie L > *Cc:* Jacob Fr?sig ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi, > > I agree. What I do is do a 3 slice sinogram from the fan-beam projections > by copying the same data in each slice but reconstruct one 2D slice. If you > need an example, I can quickly demonstrate this in a short Python script. > > Simon > > > > On Mon, May 15, 2017 at 4:01 PM, louie L wrote: > > Hi, > > > > I think you can carefully pad zeros to your projections. Reconstruct as if > it is a 3d object. Take the middle slice as your fanbeam result. > > Let me know if it helps. > > > > Best regards, > > Louie > > Sent from my iOS > > > Am 15.05.2017 um 15:55 schrieb Jacob Fr?sig : > > Dear Rtk-users > > > > I was wandering if Rtk includes an implementation of a reconstruction > method to reconstruct a 2D representation of an object given fan-beam > projections. > > Or, if anyone has experience using e.g. FDKConeBeamReconstructionFilter > on projections from line-detectors (fan-beam instead of cone-beam). > > > > I hope you guys can help. > > Yours sincerely > > *Jacob Fr?sig * > > Project Manager > Sensor Innovation > > FORCE Technology > Park All? 345 > 2605 Br?ndby > Denmark > > Phone: +45 43 25 00 00 <+45%2043%2025%2000%2000> > Direct: +45 43 25 16 43 <+45%2043%2025%2016%2043> > Skype for Business: jafs at forcetechnology.com > Fax: +45 43 25 00 10 <+45%2043%2025%2000%2010> > e-mail: jafs at force.dk > www: forcetechnology.com > > > ************************************************************************* > This email and any files transmitted with it may contain confidential > information intended for the addressee(s) only. The information is not to > be > surrendered or copied to unauthorised persons. If you have received > this communication in error, please notify us immediately by email at: > info at forcetechnology.com > ************************************************************************* > > _______________________________________________ > 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 jafs at force.dk Tue May 16 09:16:32 2017 From: jafs at force.dk (=?utf-8?B?SmFjb2IgRnLDuHNpZw==?=) Date: Tue, 16 May 2017 13:16:32 +0000 Subject: [Rtk-users] Reconstructing from fan-beam projections In-Reply-To: References: Message-ID: Hi, The attached sinogram consist of line integral values, i.e., sinogram(i,j) = -ln[ I(i,j)/I_0(i) ] where I and ?I_0 are the measured intensities with and without an object, respectively. Since we are measuring with a line detector, the ?zero? (I_0) is in this case just an array. j is the index for the projections, i.e., j ? {1,2,?,360} since we take one projection for each whole angle. I hope this explains the sinogram and again; thank you for your time! Best regards, Jacob From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: 16. maj 2017 14:54 To: Jacob Fr?sig Cc: rtk-users at openrtk.org Subject: Re: [Rtk-users] Reconstructing from fan-beam projections Hi Jacob, Thanks for the image of the sinogram. I don't understand this sinogram. Do you know how to convert each pixel value to a line integral? I.e., if it's x-ray imaging, do you have an image without object? Thanks, Simon On Tue, May 16, 2017 at 2:24 PM, Jacob Fr?sig > wrote: Hi again, and thank you for the example! I have some trouble getting a proper reconstruction. If you have the time, any help would be appreciated. Attached is my fan-beam sinogram as a .tif file. Here, projections are taken for 360 degrees and the detector has 507 pixels. I believe the issue lies in setting the geometry and maybe the spacing between the pixels. The measurement geometry is as follows Source to centre: 590 mm Source to detector: 1000 mm Detector length: 411mm Best regards, Jacob From: Rtk-users [mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Simon Rit Sent: 15. maj 2017 17:32 To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Reconstructing from fan-beam projections Hi, I have added an example here: http://wiki.openrtk.org/index.php/FanBeam The values in the first and the third rows are not used, as illustrated in this example. We add them to do a 2D interpolation but we do this 2D interpolation exactly on the second row so that's not a problem. Note that it's a bit more tricky for iterative recon but we also have a solution for this if you need it. Best regards, Simon On Mon, May 15, 2017 at 4:31 PM, Jacob Fr?sig > wrote: Hi again, Thank you for the quick answer! An example would be great, thanks. I have one concern about copying the fan-beam data: Then we would have 2D projections for which each column is the same fan-beam projection. By this, values of the same row are equal even though the cone-beam geometry indicates the outer columns correspond to intensities of rays with longer travel time through the object and hence should have attenuated more. Is this neglectable? Again, thanks! Best regards, Jacob From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: 15. maj 2017 16:05 To: louie L > Cc: Jacob Fr?sig >; rtk-users at public.kitware.com Subject: Re: [Rtk-users] Reconstructing from fan-beam projections Hi, I agree. What I do is do a 3 slice sinogram from the fan-beam projections by copying the same data in each slice but reconstruct one 2D slice. If you need an example, I can quickly demonstrate this in a short Python script. Simon On Mon, May 15, 2017 at 4:01 PM, louie L > wrote: Hi, I think you can carefully pad zeros to your projections. Reconstruct as if it is a 3d object. Take the middle slice as your fanbeam result. Let me know if it helps. Best regards, Louie Sent from my iOS Am 15.05.2017 um 15:55 schrieb Jacob Fr?sig >: Dear Rtk-users I was wandering if Rtk includes an implementation of a reconstruction method to reconstruct a 2D representation of an object given fan-beam projections. Or, if anyone has experience using e.g. FDKConeBeamReconstructionFilter on projections from line-detectors (fan-beam instead of cone-beam). I hope you guys can help. Yours sincerely Jacob Fr?sig Project Manager Sensor Innovation FORCE Technology Park All? 345 2605 Br?ndby Denmark Phone: +45 43 25 00 00 Direct: +45 43 25 16 43 Skype for Business: jafs at forcetechnology.com Fax: +45 43 25 00 10 e-mail: jafs at force.dk www: forcetechnology.com ************************************************************************* This email and any files transmitted with it may contain confidential information intended for the addressee(s) only. The information is not to be surrendered or copied to unauthorised persons. If you have received this communication in error, please notify us immediately by email at: info at forcetechnology.com ************************************************************************* _______________________________________________ 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 simon.rit at creatis.insa-lyon.fr Tue May 16 10:59:12 2017 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 16 May 2017 16:59:12 +0200 Subject: [Rtk-users] Reconstructing from fan-beam projections In-Reply-To: References: Message-ID: Hi, If this is true, then the sinogram indicates that you are dealing with an interior problem since you have high line integrals at the border (see enclosed profile). Is that indeed the case? If yes, that's a difficult problem... Simon On Tue, May 16, 2017 at 3:16 PM, Jacob Fr?sig wrote: > Hi, > > > > The attached sinogram consist of line integral values, i.e., sinogram(i,j) > = -ln[ *I(i,j)/I_0(i)* ] where *I *and *?**I_0 *are the measured > intensities with and without an object, respectively. > Since we are measuring with a line detector, the ?zero? (*I_0*) is in > this case just an array. > > *j* is the index for the projections, i.e., *j* ? {1,2,?,360} since we > take one projection for each whole angle. > > I hope this explains the sinogram and again; thank you for your time! > > Best regards, > > Jacob > > > > *From:* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *On Behalf Of *Simon > Rit > *Sent:* 16. maj 2017 14:54 > *To:* Jacob Fr?sig > *Cc:* rtk-users at openrtk.org > > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi Jacob, > > Thanks for the image of the sinogram. I don't understand this sinogram. Do > you know how to convert each pixel value to a line integral? I.e., if it's > x-ray imaging, do you have an image without object? > > Thanks, > > Simon > > > > On Tue, May 16, 2017 at 2:24 PM, Jacob Fr?sig wrote: > > Hi again, > > and thank you for the example! > > I have some trouble getting a proper reconstruction. If you have the time, > any help would be appreciated. > > Attached is my fan-beam sinogram as a .tif file. Here, projections are > taken for 360 degrees and the detector has 507 pixels. > I believe the issue lies in setting the geometry and maybe the spacing > between the pixels. The measurement geometry is as follows > > Source to centre: 590 mm > > Source to detector: 1000 mm > > Detector length: 411mm > > > > Best regards, > > > > Jacob > > > > > > *From:* Rtk-users [mailto:rtk-users-bounces at public.kitware.com] *On > Behalf Of *Simon Rit > *Sent:* 15. maj 2017 17:32 > *To:* rtk-users at openrtk.org > > > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi, > > I have added an example here: > http://wiki.openrtk.org/index.php/FanBeam > > The values in the first and the third rows are not used, as illustrated in > this example. We add them to do a 2D interpolation but we do this 2D > interpolation exactly on the second row so that's not a problem. > > Note that it's a bit more tricky for iterative recon but we also have a > solution for this if you need it. > > Best regards, > > Simon > > > > On Mon, May 15, 2017 at 4:31 PM, Jacob Fr?sig wrote: > > Hi again, > > > > Thank you for the quick answer! An example would be great, thanks. I have > one concern about copying the fan-beam data: > > > Then we would have 2D projections for which each column is the same > fan-beam projection. By this, values of the same row are equal even though > the cone-beam geometry indicates the outer columns correspond to > intensities of rays with longer travel time through the object and hence > should have attenuated more. Is this neglectable? > > > > Again, thanks! > > > > Best regards, > > Jacob > > > > > > > > *From:* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *On Behalf Of *Simon > Rit > *Sent:* 15. maj 2017 16:05 > *To:* louie L > *Cc:* Jacob Fr?sig ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi, > > I agree. What I do is do a 3 slice sinogram from the fan-beam projections > by copying the same data in each slice but reconstruct one 2D slice. If you > need an example, I can quickly demonstrate this in a short Python script. > > Simon > > > > On Mon, May 15, 2017 at 4:01 PM, louie L wrote: > > Hi, > > > > I think you can carefully pad zeros to your projections. Reconstruct as if > it is a 3d object. Take the middle slice as your fanbeam result. > > Let me know if it helps. > > > > Best regards, > > Louie > > Sent from my iOS > > > Am 15.05.2017 um 15:55 schrieb Jacob Fr?sig : > > Dear Rtk-users > > > > I was wandering if Rtk includes an implementation of a reconstruction > method to reconstruct a 2D representation of an object given fan-beam > projections. > > Or, if anyone has experience using e.g. FDKConeBeamReconstructionFilter > on projections from line-detectors (fan-beam instead of cone-beam). > > > > I hope you guys can help. > > Yours sincerely > > *Jacob Fr?sig * > > Project Manager > Sensor Innovation > > FORCE Technology > Park All? 345 > 2605 Br?ndby > Denmark > > Phone: +45 43 25 00 00 <+45%2043%2025%2000%2000> > Direct: +45 43 25 16 43 <+45%2043%2025%2016%2043> > Skype for Business: jafs at forcetechnology.com > Fax: +45 43 25 00 10 <+45%2043%2025%2000%2010> > e-mail: jafs at force.dk > www: forcetechnology.com > > > ************************************************************************* > This email and any files transmitted with it may contain confidential > information intended for the addressee(s) only. The information is not to > be > surrendered or copied to unauthorised persons. If you have received > this communication in error, please notify us immediately by email at: > info at forcetechnology.com > ************************************************************************* > > _______________________________________________ > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: profile.tiff Type: image/tiff Size: 48182 bytes Desc: not available URL: From jafs at force.dk Tue May 16 13:22:00 2017 From: jafs at force.dk (=?utf-8?B?SmFjb2IgRnLDuHNpZw==?=) Date: Tue, 16 May 2017 17:22:00 +0000 Subject: [Rtk-users] Reconstructing from fan-beam projections In-Reply-To: References: , Message-ID: Hi, yes, it is indeed an interior- / region of interest problem in the sense that we only are interested in the fully illuminated centre region. I have previously had success in getting good reconstructions from interior data using variational formulation with tailored penalty term. However, this is implemented in Matlab and the aim is to use your implementation to get a C++ implementation of this method. But for now, I am just figuring how to do a simple reconstruction to get a grasp on the library. Best regards, Jacob ________________________________ Fra: simon.rit at gmail.com p? vegne af Simon Rit Sendt: 16. maj 2017 16:59:12 Til: Jacob Fr?sig Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Reconstructing from fan-beam projections Hi, If this is true, then the sinogram indicates that you are dealing with an interior problem since you have high line integrals at the border (see enclosed profile). Is that indeed the case? If yes, that's a difficult problem... Simon On Tue, May 16, 2017 at 3:16 PM, Jacob Fr?sig > wrote: Hi, The attached sinogram consist of line integral values, i.e., sinogram(i,j) = -ln[ I(i,j)/I_0(i) ] where I and ?I_0 are the measured intensities with and without an object, respectively. Since we are measuring with a line detector, the ?zero? (I_0) is in this case just an array. j is the index for the projections, i.e., j ? {1,2,?,360} since we take one projection for each whole angle. I hope this explains the sinogram and again; thank you for your time! Best regards, Jacob From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: 16. maj 2017 14:54 To: Jacob Fr?sig > Cc: rtk-users at openrtk.org Subject: Re: [Rtk-users] Reconstructing from fan-beam projections Hi Jacob, Thanks for the image of the sinogram. I don't understand this sinogram. Do you know how to convert each pixel value to a line integral? I.e., if it's x-ray imaging, do you have an image without object? Thanks, Simon On Tue, May 16, 2017 at 2:24 PM, Jacob Fr?sig > wrote: Hi again, and thank you for the example! I have some trouble getting a proper reconstruction. If you have the time, any help would be appreciated. Attached is my fan-beam sinogram as a .tif file. Here, projections are taken for 360 degrees and the detector has 507 pixels. I believe the issue lies in setting the geometry and maybe the spacing between the pixels. The measurement geometry is as follows Source to centre: 590 mm Source to detector: 1000 mm Detector length: 411mm Best regards, Jacob From: Rtk-users [mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Simon Rit Sent: 15. maj 2017 17:32 To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Reconstructing from fan-beam projections Hi, I have added an example here: http://wiki.openrtk.org/index.php/FanBeam The values in the first and the third rows are not used, as illustrated in this example. We add them to do a 2D interpolation but we do this 2D interpolation exactly on the second row so that's not a problem. Note that it's a bit more tricky for iterative recon but we also have a solution for this if you need it. Best regards, Simon On Mon, May 15, 2017 at 4:31 PM, Jacob Fr?sig > wrote: Hi again, Thank you for the quick answer! An example would be great, thanks. I have one concern about copying the fan-beam data: Then we would have 2D projections for which each column is the same fan-beam projection. By this, values of the same row are equal even though the cone-beam geometry indicates the outer columns correspond to intensities of rays with longer travel time through the object and hence should have attenuated more. Is this neglectable? Again, thanks! Best regards, Jacob From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: 15. maj 2017 16:05 To: louie L > Cc: Jacob Fr?sig >; rtk-users at public.kitware.com Subject: Re: [Rtk-users] Reconstructing from fan-beam projections Hi, I agree. What I do is do a 3 slice sinogram from the fan-beam projections by copying the same data in each slice but reconstruct one 2D slice. If you need an example, I can quickly demonstrate this in a short Python script. Simon On Mon, May 15, 2017 at 4:01 PM, louie L > wrote: Hi, I think you can carefully pad zeros to your projections. Reconstruct as if it is a 3d object. Take the middle slice as your fanbeam result. Let me know if it helps. Best regards, Louie Sent from my iOS Am 15.05.2017 um 15:55 schrieb Jacob Fr?sig >: Dear Rtk-users I was wandering if Rtk includes an implementation of a reconstruction method to reconstruct a 2D representation of an object given fan-beam projections. Or, if anyone has experience using e.g. FDKConeBeamReconstructionFilter on projections from line-detectors (fan-beam instead of cone-beam). I hope you guys can help. Yours sincerely Jacob Fr?sig Project Manager Sensor Innovation FORCE Technology Park All? 345 2605 Br?ndby Denmark Phone: +45 43 25 00 00 Direct: +45 43 25 16 43 Skype for Business: jafs at forcetechnology.com Fax: +45 43 25 00 10 e-mail: jafs at force.dk www: forcetechnology.com ************************************************************************* This email and any files transmitted with it may contain confidential information intended for the addressee(s) only. The information is not to be surrendered or copied to unauthorised persons. If you have received this communication in error, please notify us immediately by email at: info at forcetechnology.com ************************************************************************* _______________________________________________ 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 simon.rit at creatis.insa-lyon.fr Wed May 17 10:41:34 2017 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 17 May 2017 16:41:34 +0200 Subject: [Rtk-users] Reconstructing from fan-beam projections In-Reply-To: References: Message-ID: I guess the extreme negative values are due to truncation. I have never worked on the interior problem before so I don't have experience with this but I'm not surprised that you reconstruct bad values. The implemented correction is Ohnesorge, B.; Flohr, T.; Schwarz, K.; Heiken, J. & Bae, K. Efficient correction for CT image artifacts caused by objects extending outside the scan field of view *Med Phys, **2000**, 27*, 39-46 The parameter is the ratio of extension (between 0 and 1). Simon On Wed, May 17, 2017 at 3:41 PM, Jacob Fr?sig wrote: > Hi, > > > > Thank you, it is a great help! Attached is a report describing the project > where the beginning of chapter 5 describes the data acquisition. > The investigated object is an oil pipe. Yes, the reconstruction contains > the expected interior part of the oil pipe along with the ring artefact > > which is characteristic for the interior problem. > What puzzles me is that I get a few extreme negative values, -1.5884e+38 > , in the bottom of the reconstruction using FDKConeBeamReconstructionFilte > r. I have attached the truncated reconstruction without negative values > and the reconstruction with negative values. What exactly is your > truncation correction? > > Have you seen something similar before? > > > > Best regards, > > > > Jacob > > > > *From:* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *On Behalf Of *Simon > Rit > *Sent:* 17. maj 2017 15:03 > > *To:* Jacob Fr?sig > *Cc:* rtk-users at openrtk.org > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi, > > Here is what I obtain. I have no clue what you expect but that's how I > would translate the geometric information that you provided. The interior > problem is obviously an issue here (our truncation correction does not help > for interior CT) but maybe you can tell us if you recognize your object. > There are clear ring artefacts as well in your sinogram. > > I hope this helps, > > Simon > > > > On Tue, May 16, 2017 at 7:22 PM, Jacob Fr?sig wrote: > > Hi, > > > > yes, it is indeed an interior- / region of interest problem in the sense > that we only are interested in the fully illuminated centre region. > I have previously had success in getting good reconstructions from > interior data using variational formulation with tailored penalty term. > However, this is implemented in Matlab and the aim is to use your > implementation to get a C++ implementation of this method. > > But for now, I am just figuring how to do a simple reconstruction to get a > grasp on the library. > > > > Best regards, > > > > Jacob > > > > > ------------------------------ > > *Fra:* simon.rit at gmail.com p? vegne af Simon Rit < > simon.rit at creatis.insa-lyon.fr> > *Sendt:* 16. maj 2017 16:59:12 > *Til:* Jacob Fr?sig > *Cc:* rtk-users at openrtk.org > *Emne:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi, > > If this is true, then the sinogram indicates that you are dealing with an > interior problem since you have high line integrals at the border (see > enclosed profile). Is that indeed the case? If yes, that's a difficult > problem... > > Simon > > > > On Tue, May 16, 2017 at 3:16 PM, Jacob Fr?sig wrote: > > Hi, > > > > The attached sinogram consist of line integral values, i.e., sinogram(i,j) > = -ln[ *I(i,j)/I_0(i)* ] where *I *and *?**I_0 *are the measured > intensities with and without an object, respectively. > Since we are measuring with a line detector, the ?zero? (*I_0*) is in > this case just an array. > > *j* is the index for the projections, i.e., *j* ? {1,2,?,360} since we > take one projection for each whole angle. > > I hope this explains the sinogram and again; thank you for your time! > > Best regards, > > Jacob > > > > *From:* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *On Behalf Of *Simon > Rit > *Sent:* 16. maj 2017 14:54 > *To:* Jacob Fr?sig > *Cc:* rtk-users at openrtk.org > > > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi Jacob, > > Thanks for the image of the sinogram. I don't understand this sinogram. Do > you know how to convert each pixel value to a line integral? I.e., if it's > x-ray imaging, do you have an image without object? > > Thanks, > > Simon > > > > On Tue, May 16, 2017 at 2:24 PM, Jacob Fr?sig wrote: > > Hi again, > > and thank you for the example! > > I have some trouble getting a proper reconstruction. If you have the time, > any help would be appreciated. > > Attached is my fan-beam sinogram as a .tif file. Here, projections are > taken for 360 degrees and the detector has 507 pixels. > I believe the issue lies in setting the geometry and maybe the spacing > between the pixels. The measurement geometry is as follows > > Source to centre: 590 mm > > Source to detector: 1000 mm > > Detector length: 411mm > > > > Best regards, > > > > Jacob > > > > > > *From:* Rtk-users [mailto:rtk-users-bounces at public.kitware.com] *On > Behalf Of *Simon Rit > *Sent:* 15. maj 2017 17:32 > *To:* rtk-users at openrtk.org > > > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi, > > I have added an example here: > http://wiki.openrtk.org/index.php/FanBeam > > The values in the first and the third rows are not used, as illustrated in > this example. We add them to do a 2D interpolation but we do this 2D > interpolation exactly on the second row so that's not a problem. > > Note that it's a bit more tricky for iterative recon but we also have a > solution for this if you need it. > > Best regards, > > Simon > > > > On Mon, May 15, 2017 at 4:31 PM, Jacob Fr?sig wrote: > > Hi again, > > > > Thank you for the quick answer! An example would be great, thanks. I have > one concern about copying the fan-beam data: > > > Then we would have 2D projections for which each column is the same > fan-beam projection. By this, values of the same row are equal even though > the cone-beam geometry indicates the outer columns correspond to > intensities of rays with longer travel time through the object and hence > should have attenuated more. Is this neglectable? > > > > Again, thanks! > > > > Best regards, > > Jacob > > > > > > > > *From:* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *On Behalf Of *Simon > Rit > *Sent:* 15. maj 2017 16:05 > *To:* louie L > *Cc:* Jacob Fr?sig ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi, > > I agree. What I do is do a 3 slice sinogram from the fan-beam projections > by copying the same data in each slice but reconstruct one 2D slice. If you > need an example, I can quickly demonstrate this in a short Python script. > > Simon > > > > On Mon, May 15, 2017 at 4:01 PM, louie L wrote: > > Hi, > > > > I think you can carefully pad zeros to your projections. Reconstruct as if > it is a 3d object. Take the middle slice as your fanbeam result. > > Let me know if it helps. > > > > Best regards, > > Louie > > Sent from my iOS > > > Am 15.05.2017 um 15:55 schrieb Jacob Fr?sig : > > Dear Rtk-users > > > > I was wandering if Rtk includes an implementation of a reconstruction > method to reconstruct a 2D representation of an object given fan-beam > projections. > > Or, if anyone has experience using e.g. FDKConeBeamReconstructionFilter > on projections from line-detectors (fan-beam instead of cone-beam). > > > > I hope you guys can help. > > Yours sincerely > > *Jacob Fr?sig * > > Project Manager > Sensor Innovation > > FORCE Technology > Park All? 345 > 2605 Br?ndby > Denmark > > Phone: +45 43 25 00 00 <+45%2043%2025%2000%2000> > Direct: +45 43 25 16 43 <+45%2043%2025%2016%2043> > Skype for Business: jafs at forcetechnology.com > Fax: +45 43 25 00 10 <+45%2043%2025%2000%2010> > e-mail: jafs at force.dk > www: forcetechnology.com > > > ************************************************************************* > This email and any files transmitted with it may contain confidential > information intended for the addressee(s) only. The information is not to > be > surrendered or copied to unauthorised persons. If you have received > this communication in error, please notify us immediately by email at: > info at forcetechnology.com > ************************************************************************* > > _______________________________________________ > 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 jafs at force.dk Thu May 18 04:20:57 2017 From: jafs at force.dk (=?utf-8?B?SmFjb2IgRnLDuHNpZw==?=) Date: Thu, 18 May 2017 08:20:57 +0000 Subject: [Rtk-users] Reconstructing from fan-beam projections In-Reply-To: References: Message-ID: Hi, Thank you for the input and reference! You previously mentioned that there was a method to use the iterative reconstructions for fanbeam measurements. What is exactly needed? And is it similar for the ADMM wavelet reconstruction? Best regards, Jacob From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: 17. maj 2017 16:42 To: Jacob Fr?sig Cc: rtk-users at openrtk.org Subject: Re: [Rtk-users] Reconstructing from fan-beam projections I guess the extreme negative values are due to truncation. I have never worked on the interior problem before so I don't have experience with this but I'm not surprised that you reconstruct bad values. The implemented correction is Ohnesorge, B.; Flohr, T.; Schwarz, K.; Heiken, J. & Bae, K. Efficient correction for CT image artifacts caused by objects extending outside the scan field of view Med Phys, 2000, 27, 39-46 The parameter is the ratio of extension (between 0 and 1). Simon On Wed, May 17, 2017 at 3:41 PM, Jacob Fr?sig > wrote: Hi, Thank you, it is a great help! Attached is a report describing the project where the beginning of chapter 5 describes the data acquisition. The investigated object is an oil pipe. Yes, the reconstruction contains the expected interior part of the oil pipe along with the ring artefact which is characteristic for the interior problem. What puzzles me is that I get a few extreme negative values, -1.5884e+38 , in the bottom of the reconstruction using FDKConeBeamReconstructionFilter. I have attached the truncated reconstruction without negative values and the reconstruction with negative values. What exactly is your truncation correction? Have you seen something similar before? Best regards, Jacob From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: 17. maj 2017 15:03 To: Jacob Fr?sig > Cc: rtk-users at openrtk.org Subject: Re: [Rtk-users] Reconstructing from fan-beam projections Hi, Here is what I obtain. I have no clue what you expect but that's how I would translate the geometric information that you provided. The interior problem is obviously an issue here (our truncation correction does not help for interior CT) but maybe you can tell us if you recognize your object. There are clear ring artefacts as well in your sinogram. I hope this helps, Simon On Tue, May 16, 2017 at 7:22 PM, Jacob Fr?sig > wrote: Hi, yes, it is indeed an interior- / region of interest problem in the sense that we only are interested in the fully illuminated centre region. I have previously had success in getting good reconstructions from interior data using variational formulation with tailored penalty term. However, this is implemented in Matlab and the aim is to use your implementation to get a C++ implementation of this method. But for now, I am just figuring how to do a simple reconstruction to get a grasp on the library. Best regards, Jacob ________________________________ Fra: simon.rit at gmail.com > p? vegne af Simon Rit > Sendt: 16. maj 2017 16:59:12 Til: Jacob Fr?sig Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Reconstructing from fan-beam projections Hi, If this is true, then the sinogram indicates that you are dealing with an interior problem since you have high line integrals at the border (see enclosed profile). Is that indeed the case? If yes, that's a difficult problem... Simon On Tue, May 16, 2017 at 3:16 PM, Jacob Fr?sig > wrote: Hi, The attached sinogram consist of line integral values, i.e., sinogram(i,j) = -ln[ I(i,j)/I_0(i) ] where I and ?I_0 are the measured intensities with and without an object, respectively. Since we are measuring with a line detector, the ?zero? (I_0) is in this case just an array. j is the index for the projections, i.e., j ? {1,2,?,360} since we take one projection for each whole angle. I hope this explains the sinogram and again; thank you for your time! Best regards, Jacob From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: 16. maj 2017 14:54 To: Jacob Fr?sig > Cc: rtk-users at openrtk.org Subject: Re: [Rtk-users] Reconstructing from fan-beam projections Hi Jacob, Thanks for the image of the sinogram. I don't understand this sinogram. Do you know how to convert each pixel value to a line integral? I.e., if it's x-ray imaging, do you have an image without object? Thanks, Simon On Tue, May 16, 2017 at 2:24 PM, Jacob Fr?sig > wrote: Hi again, and thank you for the example! I have some trouble getting a proper reconstruction. If you have the time, any help would be appreciated. Attached is my fan-beam sinogram as a .tif file. Here, projections are taken for 360 degrees and the detector has 507 pixels. I believe the issue lies in setting the geometry and maybe the spacing between the pixels. The measurement geometry is as follows Source to centre: 590 mm Source to detector: 1000 mm Detector length: 411mm Best regards, Jacob From: Rtk-users [mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Simon Rit Sent: 15. maj 2017 17:32 To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Reconstructing from fan-beam projections Hi, I have added an example here: http://wiki.openrtk.org/index.php/FanBeam The values in the first and the third rows are not used, as illustrated in this example. We add them to do a 2D interpolation but we do this 2D interpolation exactly on the second row so that's not a problem. Note that it's a bit more tricky for iterative recon but we also have a solution for this if you need it. Best regards, Simon On Mon, May 15, 2017 at 4:31 PM, Jacob Fr?sig > wrote: Hi again, Thank you for the quick answer! An example would be great, thanks. I have one concern about copying the fan-beam data: Then we would have 2D projections for which each column is the same fan-beam projection. By this, values of the same row are equal even though the cone-beam geometry indicates the outer columns correspond to intensities of rays with longer travel time through the object and hence should have attenuated more. Is this neglectable? Again, thanks! Best regards, Jacob From: simon.rit at gmail.com [mailto:simon.rit at gmail.com] On Behalf Of Simon Rit Sent: 15. maj 2017 16:05 To: louie L > Cc: Jacob Fr?sig >; rtk-users at public.kitware.com Subject: Re: [Rtk-users] Reconstructing from fan-beam projections Hi, I agree. What I do is do a 3 slice sinogram from the fan-beam projections by copying the same data in each slice but reconstruct one 2D slice. If you need an example, I can quickly demonstrate this in a short Python script. Simon On Mon, May 15, 2017 at 4:01 PM, louie L > wrote: Hi, I think you can carefully pad zeros to your projections. Reconstruct as if it is a 3d object. Take the middle slice as your fanbeam result. Let me know if it helps. Best regards, Louie Sent from my iOS Am 15.05.2017 um 15:55 schrieb Jacob Fr?sig >: Dear Rtk-users I was wandering if Rtk includes an implementation of a reconstruction method to reconstruct a 2D representation of an object given fan-beam projections. Or, if anyone has experience using e.g. FDKConeBeamReconstructionFilter on projections from line-detectors (fan-beam instead of cone-beam). I hope you guys can help. Yours sincerely Jacob Fr?sig Project Manager Sensor Innovation FORCE Technology Park All? 345 2605 Br?ndby Denmark Phone: +45 43 25 00 00 Direct: +45 43 25 16 43 Skype for Business: jafs at forcetechnology.com Fax: +45 43 25 00 10 e-mail: jafs at force.dk www: forcetechnology.com ************************************************************************* This email and any files transmitted with it may contain confidential information intended for the addressee(s) only. The information is not to be surrendered or copied to unauthorised persons. If you have received this communication in error, please notify us immediately by email at: info at forcetechnology.com ************************************************************************* _______________________________________________ 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 simon.rit at creatis.insa-lyon.fr Thu May 18 05:32:03 2017 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 18 May 2017 11:32:03 +0200 Subject: [Rtk-users] Reconstructing from fan-beam projections In-Reply-To: References: Message-ID: Hi, For iterative reconstruction, it's almost the opposite: since we use a ray-based projector, the volume needs to be 3D (and cannot be purely 2D) but the projections can be 1D. For the backprojection, you then need to have the adjoint of the projector, a voxel projector would not work. Enclosed is an example with conjugate gradient on your data but any iterative algorithm in RTK will work if you respect these projectors. Not all of them are wrapped in Python but you can write the geometry file and call them from the command line. I have added the example with simulations to the wiki: http://wiki.openrtk.org/index.php/FanBeam Simon On Thu, May 18, 2017 at 10:20 AM, Jacob Fr?sig wrote: > Hi, > > Thank you for the input and reference! > > You previously mentioned that there was a method to use the iterative > reconstructions for fanbeam measurements. What is exactly needed? And is it > similar for the ADMM wavelet reconstruction? > > > > Best regards, > > > > Jacob > > *From:* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *On Behalf Of *Simon > Rit > *Sent:* 17. maj 2017 16:42 > > *To:* Jacob Fr?sig > *Cc:* rtk-users at openrtk.org > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > I guess the extreme negative values are due to truncation. I have never > worked on the interior problem before so I don't have experience with this > but I'm not surprised that you reconstruct bad values. > The implemented correction is > Ohnesorge, B.; Flohr, T.; Schwarz, K.; Heiken, J. & Bae, K. > Efficient correction for CT image artifacts caused by objects extending > outside the scan field of view > *Med Phys, **2000**, 27*, 39-46 > > The parameter is the ratio of extension (between 0 and 1). > > Simon > > > > On Wed, May 17, 2017 at 3:41 PM, Jacob Fr?sig wrote: > > Hi, > > > > Thank you, it is a great help! Attached is a report describing the project > where the beginning of chapter 5 describes the data acquisition. > The investigated object is an oil pipe. Yes, the reconstruction contains > the expected interior part of the oil pipe along with the ring artefact > > which is characteristic for the interior problem. > What puzzles me is that I get a few extreme negative values, -1.5884e+38 > , in the bottom of the reconstruction using FDKConeBeamReconstructionFilte > r. I have attached the truncated reconstruction without negative values > and the reconstruction with negative values. What exactly is your > truncation correction? > > Have you seen something similar before? > > > > Best regards, > > > > Jacob > > > > *From:* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *On Behalf Of *Simon > Rit > *Sent:* 17. maj 2017 15:03 > > > *To:* Jacob Fr?sig > *Cc:* rtk-users at openrtk.org > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi, > > Here is what I obtain. I have no clue what you expect but that's how I > would translate the geometric information that you provided. The interior > problem is obviously an issue here (our truncation correction does not help > for interior CT) but maybe you can tell us if you recognize your object. > There are clear ring artefacts as well in your sinogram. > > I hope this helps, > > Simon > > > > On Tue, May 16, 2017 at 7:22 PM, Jacob Fr?sig wrote: > > Hi, > > > > yes, it is indeed an interior- / region of interest problem in the sense > that we only are interested in the fully illuminated centre region. > I have previously had success in getting good reconstructions from > interior data using variational formulation with tailored penalty term. > However, this is implemented in Matlab and the aim is to use your > implementation to get a C++ implementation of this method. > > But for now, I am just figuring how to do a simple reconstruction to get a > grasp on the library. > > > > Best regards, > > > > Jacob > > > > > ------------------------------ > > *Fra:* simon.rit at gmail.com p? vegne af Simon Rit < > simon.rit at creatis.insa-lyon.fr> > *Sendt:* 16. maj 2017 16:59:12 > *Til:* Jacob Fr?sig > *Cc:* rtk-users at openrtk.org > *Emne:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi, > > If this is true, then the sinogram indicates that you are dealing with an > interior problem since you have high line integrals at the border (see > enclosed profile). Is that indeed the case? If yes, that's a difficult > problem... > > Simon > > > > On Tue, May 16, 2017 at 3:16 PM, Jacob Fr?sig wrote: > > Hi, > > > > The attached sinogram consist of line integral values, i.e., sinogram(i,j) > = -ln[ *I(i,j)/I_0(i)* ] where *I *and *?**I_0 *are the measured > intensities with and without an object, respectively. > Since we are measuring with a line detector, the ?zero? (*I_0*) is in > this case just an array. > > *j* is the index for the projections, i.e., *j* ? {1,2,?,360} since we > take one projection for each whole angle. > > I hope this explains the sinogram and again; thank you for your time! > > Best regards, > > Jacob > > > > *From:* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *On Behalf Of *Simon > Rit > *Sent:* 16. maj 2017 14:54 > *To:* Jacob Fr?sig > *Cc:* rtk-users at openrtk.org > > > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi Jacob, > > Thanks for the image of the sinogram. I don't understand this sinogram. Do > you know how to convert each pixel value to a line integral? I.e., if it's > x-ray imaging, do you have an image without object? > > Thanks, > > Simon > > > > On Tue, May 16, 2017 at 2:24 PM, Jacob Fr?sig wrote: > > Hi again, > > and thank you for the example! > > I have some trouble getting a proper reconstruction. If you have the time, > any help would be appreciated. > > Attached is my fan-beam sinogram as a .tif file. Here, projections are > taken for 360 degrees and the detector has 507 pixels. > I believe the issue lies in setting the geometry and maybe the spacing > between the pixels. The measurement geometry is as follows > > Source to centre: 590 mm > > Source to detector: 1000 mm > > Detector length: 411mm > > > > Best regards, > > > > Jacob > > > > > > *From:* Rtk-users [mailto:rtk-users-bounces at public.kitware.com] *On > Behalf Of *Simon Rit > *Sent:* 15. maj 2017 17:32 > *To:* rtk-users at openrtk.org > > > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi, > > I have added an example here: > http://wiki.openrtk.org/index.php/FanBeam > > The values in the first and the third rows are not used, as illustrated in > this example. We add them to do a 2D interpolation but we do this 2D > interpolation exactly on the second row so that's not a problem. > > Note that it's a bit more tricky for iterative recon but we also have a > solution for this if you need it. > > Best regards, > > Simon > > > > On Mon, May 15, 2017 at 4:31 PM, Jacob Fr?sig wrote: > > Hi again, > > > > Thank you for the quick answer! An example would be great, thanks. I have > one concern about copying the fan-beam data: > > > Then we would have 2D projections for which each column is the same > fan-beam projection. By this, values of the same row are equal even though > the cone-beam geometry indicates the outer columns correspond to > intensities of rays with longer travel time through the object and hence > should have attenuated more. Is this neglectable? > > > > Again, thanks! > > > > Best regards, > > Jacob > > > > > > > > *From:* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *On Behalf Of *Simon > Rit > *Sent:* 15. maj 2017 16:05 > *To:* louie L > *Cc:* Jacob Fr?sig ; rtk-users at public.kitware.com > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections > > > > Hi, > > I agree. What I do is do a 3 slice sinogram from the fan-beam projections > by copying the same data in each slice but reconstruct one 2D slice. If you > need an example, I can quickly demonstrate this in a short Python script. > > Simon > > > > On Mon, May 15, 2017 at 4:01 PM, louie L wrote: > > Hi, > > > > I think you can carefully pad zeros to your projections. Reconstruct as if > it is a 3d object. Take the middle slice as your fanbeam result. > > Let me know if it helps. > > > > Best regards, > > Louie > > Sent from my iOS > > > Am 15.05.2017 um 15:55 schrieb Jacob Fr?sig : > > Dear Rtk-users > > > > I was wandering if Rtk includes an implementation of a reconstruction > method to reconstruct a 2D representation of an object given fan-beam > projections. > > Or, if anyone has experience using e.g. FDKConeBeamReconstructionFilter > on projections from line-detectors (fan-beam instead of cone-beam). > > > > I hope you guys can help. > > Yours sincerely > > *Jacob Fr?sig * > > Project Manager > Sensor Innovation > > FORCE Technology > Park All? 345 > 2605 Br?ndby > Denmark > > Phone: +45 43 25 00 00 <+45%2043%2025%2000%2000> > Direct: +45 43 25 16 43 <+45%2043%2025%2016%2043> > Skype for Business: jafs at forcetechnology.com > Fax: +45 43 25 00 10 <+45%2043%2025%2000%2010> > e-mail: jafs at force.dk > www: forcetechnology.com > > > ************************************************************************* > This email and any files transmitted with it may contain confidential > information intended for the addressee(s) only. The information is not to > be > surrendered or copied to unauthorised persons. If you have received > this communication in error, please notify us immediately by email at: > info at forcetechnology.com > ************************************************************************* > > _______________________________________________ > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: fanbeam_cg.py Type: text/x-python-script Size: 1311 bytes Desc: not available URL: From DMEDMUNDS at mgh.harvard.edu Thu May 18 15:14:18 2017 From: DMEDMUNDS at mgh.harvard.edu (Edmunds, David Michael) Date: Thu, 18 May 2017 19:14:18 +0000 Subject: [Rtk-users] On the fly CBCT reconstruction Message-ID: <3DB53C5A15F5A745A0B03B9BEE4FAC3014162557@PHSX10MB12.partners.org> Hi all, I am investigating options for performing on the fly CBCT reconstruction, i.e. beginning the reconstruction as soon as the first projection image arrives and integrating new projections as they arrive in parallel. Is there much support for this kind of functionality in RTK? So far, I have found the "rtkinlinefdk" application source code, but I don't think this does exactly what I need. Are there any other options? Kind regards, Dave Edmunds The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri May 19 05:07:16 2017 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 19 May 2017 11:07:16 +0200 Subject: [Rtk-users] On the fly CBCT reconstruction In-Reply-To: <3DB53C5A15F5A745A0B03B9BEE4FAC3014162557@PHSX10MB12.partners.org> References: <3DB53C5A15F5A745A0B03B9BEE4FAC3014162557@PHSX10MB12.partners.org> Message-ID: Hi, This is exactly what this code demonstrates on simulated data. One thread takes care on the online reconstruction (InlineThreadCallback) and the other fills in a stack every time you have a new projection (AcquisitionCallback). Why do you think it does not exactly that? Other RTK users (mainly companies) have implemented this in different manners but the idea is there. Simon On Thu, May 18, 2017 at 9:14 PM, Edmunds, David Michael wrote: > Hi all, > > > > I am investigating options for performing on the fly CBCT reconstruction, > i.e. beginning the reconstruction as soon as the first projection image > arrives and integrating new projections as they arrive in parallel. Is there > much support for this kind of functionality in RTK? So far, I have found the > ?rtkinlinefdk? application source code, but I don?t think this does exactly > what I need. Are there any other options? > > > > Kind regards, > > > > Dave Edmunds > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users >