From lars-friedrich at gmx.net Thu Aug 17 08:40:21 2017 From: lars-friedrich at gmx.net (Lars Friedrich Lars) Date: Thu, 17 Aug 2017 14:40:21 +0200 Subject: [Rtk-users] job offer: X-ray / (CB)CT imaging experts Message-ID: An HTML attachment was scrubbed... URL: From samuel.gerber at kitware.com Thu Aug 17 09:45:19 2017 From: samuel.gerber at kitware.com (Samuel Gerber) Date: Thu, 17 Aug 2017 09:45:19 -0400 Subject: [Rtk-users] Projection Geometry and Image Origins Message-ID: Hi, I'm curious about the settings for the different origins when setting up a ProjectionGeometry, in particular ThreeDCircularProjectionGeometry. As far as I understand there is three origins: - The projection geometry origin at (0, 0, 0) - The input image origin - The projection image origin In order to center the projection on the input image I assume that I will have to use the offset parameters to shift the source and detector so that they are centered on the input image in physical coordinates. How does the projection image origin come into play? Thanks Samuel -- Samuel Gerber R&D Engineer Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Aug 18 02:53:07 2017 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 18 Aug 2017 08:53:07 +0200 Subject: [Rtk-users] Projection Geometry and Image Origins In-Reply-To: References: Message-ID: Dear Samuel, Here is how I'd explain it: there are two ITK images, a volume and a stack of projections. Each image has its own coordinate system, defined in ITK by the Origin, the Spacing and the Direction. The geometry links the volume coordinate system to each projection coordinate system (which is common for all projections) of the stack using 9 parameters per projection. In order to center the volume on the projections, you have different scenarios. Let's take one example: - the volume is centered around (0,0,0) (e.g., origin=(-127,-127,-127), spacing=(2,2,2) and size=(128,128,128)), - the projection is centered around (0,0) (e.g., same values as for the volume. Note that the third coordinate is ignored by RTK). - then the projection is centered on the volume if all offsets are 0. If the projection had not been centered (e.g., origin=(0,0,0)), then you can create exactly the same geometry by setting ProjectionOffsetX=ProjectionOffsetY=127. I hope this helps, Simon On Thu, Aug 17, 2017 at 3:45 PM, Samuel Gerber wrote: > Hi, > > I'm curious about the settings for the different origins when setting up a > ProjectionGeometry, in particular ThreeDCircularProjectionGeometry. > > As far as I understand there is three origins: > - The projection geometry origin at (0, 0, 0) > - The input image origin > - The projection image origin > > In order to center the projection on the input image I assume that I will > have to use the offset parameters to shift the source and detector so that > they are centered on the input image in physical coordinates. > How does the projection image origin come into play? > > Thanks > Samuel > > -- > Samuel Gerber > R&D Engineer > Kitware, Inc. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From samuel.gerber at kitware.com Fri Aug 18 10:03:29 2017 From: samuel.gerber at kitware.com (Samuel Gerber) Date: Fri, 18 Aug 2017 10:03:29 -0400 Subject: [Rtk-users] Fwd: Projection Geometry and Image Origins In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: Samuel Gerber Date: Fri, Aug 18, 2017 at 10:01 AM Subject: Re: [Rtk-users] Projection Geometry and Image Origins To: Simon Rit Thank you Simon. One more clarification question Are the SID and SDD parameters measured in units of the input volume spacing in z? On Fri, Aug 18, 2017 at 2:53 AM, Simon Rit wrote: > Dear Samuel, > Here is how I'd explain it: there are two ITK images, a volume and a > stack of projections. Each image has its own coordinate system, > defined in ITK by the Origin, the Spacing and the Direction. The > geometry links the volume coordinate system to each projection > coordinate system (which is common for all projections) of the stack > using 9 parameters per projection. > In order to center the volume on the projections, you have different > scenarios. Let's take one example: > - the volume is centered around (0,0,0) (e.g., > origin=(-127,-127,-127), spacing=(2,2,2) and size=(128,128,128)), > - the projection is centered around (0,0) (e.g., same values as for > the volume. Note that the third coordinate is ignored by RTK). > - then the projection is centered on the volume if all offsets are 0. > If the projection had not been centered (e.g., origin=(0,0,0)), then > you can create exactly the same geometry by setting > ProjectionOffsetX=ProjectionOffsetY=127. > I hope this helps, > Simon > > On Thu, Aug 17, 2017 at 3:45 PM, Samuel Gerber > wrote: > > Hi, > > > > I'm curious about the settings for the different origins when setting up > a > > ProjectionGeometry, in particular ThreeDCircularProjectionGeometry. > > > > As far as I understand there is three origins: > > - The projection geometry origin at (0, 0, 0) > > - The input image origin > > - The projection image origin > > > > In order to center the projection on the input image I assume that I will > > have to use the offset parameters to shift the source and detector so > that > > they are centered on the input image in physical coordinates. > > How does the projection image origin come into play? > > > > Thanks > > Samuel > > > > -- > > Samuel Gerber > > R&D Engineer > > Kitware, Inc. > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > -- Samuel Gerber R&D Engineer Kitware, Inc. -- Samuel Gerber R&D Engineer Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Aug 18 11:54:37 2017 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 18 Aug 2017 17:54:37 +0200 Subject: [Rtk-users] Fwd: Projection Geometry and Image Origins In-Reply-To: References: Message-ID: All distances in the geometry file are in the same unit as the image spacing (i.e., mm in most cases). I forgot to mention the geometry doc before http://www.openrtk.org/Doxygen/geometry.pdf On Fri, Aug 18, 2017 at 4:03 PM, Samuel Gerber wrote: > > ---------- Forwarded message ---------- > From: Samuel Gerber > Date: Fri, Aug 18, 2017 at 10:01 AM > Subject: Re: [Rtk-users] Projection Geometry and Image Origins > To: Simon Rit > > > Thank you Simon. > > One more clarification question Are the SID and SDD parameters measured in > units of the input volume spacing in z? > > > On Fri, Aug 18, 2017 at 2:53 AM, Simon Rit > wrote: > >> Dear Samuel, >> Here is how I'd explain it: there are two ITK images, a volume and a >> stack of projections. Each image has its own coordinate system, >> defined in ITK by the Origin, the Spacing and the Direction. The >> geometry links the volume coordinate system to each projection >> coordinate system (which is common for all projections) of the stack >> using 9 parameters per projection. >> In order to center the volume on the projections, you have different >> scenarios. Let's take one example: >> - the volume is centered around (0,0,0) (e.g., >> origin=(-127,-127,-127), spacing=(2,2,2) and size=(128,128,128)), >> - the projection is centered around (0,0) (e.g., same values as for >> the volume. Note that the third coordinate is ignored by RTK). >> - then the projection is centered on the volume if all offsets are 0. >> If the projection had not been centered (e.g., origin=(0,0,0)), then >> you can create exactly the same geometry by setting >> ProjectionOffsetX=ProjectionOffsetY=127. >> I hope this helps, >> Simon >> >> On Thu, Aug 17, 2017 at 3:45 PM, Samuel Gerber >> wrote: >> > Hi, >> > >> > I'm curious about the settings for the different origins when setting >> up a >> > ProjectionGeometry, in particular ThreeDCircularProjectionGeometry. >> > >> > As far as I understand there is three origins: >> > - The projection geometry origin at (0, 0, 0) >> > - The input image origin >> > - The projection image origin >> > >> > In order to center the projection on the input image I assume that I >> will >> > have to use the offset parameters to shift the source and detector so >> that >> > they are centered on the input image in physical coordinates. >> > How does the projection image origin come into play? >> > >> > Thanks >> > Samuel >> > >> > -- >> > Samuel Gerber >> > R&D Engineer >> > Kitware, Inc. >> > >> > _______________________________________________ >> > Rtk-users mailing list >> > Rtk-users at public.kitware.com >> > http://public.kitware.com/mailman/listinfo/rtk-users >> > >> > > > > -- > Samuel Gerber > R&D Engineer > Kitware, Inc. > > > > -- > Samuel Gerber > R&D Engineer > Kitware, Inc. > > _______________________________________________ > 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 Fri Aug 25 03:32:52 2017 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 25 Aug 2017 09:32:52 +0200 Subject: [Rtk-users] CBCT projection values In-Reply-To: References: Message-ID: Dear Atallah, Please use the mailing list for questions that can interest other users. The values in the his files are the raw projections after flat field correction. The value of I0 is not provided by Elekta. RTK currently uses a fixed I0 equal to 65535 but this is probably not accurate. Best regards, Simon On 23/08/2017 17:52, Atallah Baydoun wrote: > Hello, > > I am reaching you after doing some online search for RTK users. > > I am a PhD student at CWRU and I have started working on some CBCT > data from Elekta XVI. > > I was able to get a projection data and read the his file in Matlab. > I am not able however to interpret the numbers I get in the 512*512 > matrix. > > How are these numbers related to the value of projection I/I0? > > I know that the question might sound simple but I will be really > grateful for your help. > > Thank you, > > *Atallah Baydoun, MD*/ > PhD Student - Department of Biomedical Engineering, Case Western > Reserve University, Cleveland, Ohio > Email: axb724 at case.edu > Pager: 440 562 0745 / -------------- next part -------------- An HTML attachment was scrubbed... URL: From anavaniqui at gmail.com Wed Aug 30 05:46:21 2017 From: anavaniqui at gmail.com (ana) Date: Wed, 30 Aug 2017 11:46:21 +0200 Subject: [Rtk-users] SIRT Reconstruction Message-ID: Hi, I was wondering if you guys had the opportunity to look into SIRT reconstruction. There was a thread on this topic on July 27th, in which a user, Lotte, described her results after 100 iterations. I am having the same issue myself. The SART reconstruction works perfectly fine but even after 100 iterations, SIRT does not seem to improve. Regarding the example presented before, do you have any advice on how to improve it? Thank you very much. Kind regards, Ana -------------- next part -------------- An HTML attachment was scrubbed... URL: