Re: [Rtk-users] CUDA projections are blank

ointer filter = FilterType::New(); >>> filter -> SetInput(image); >>> filter -> SetOutputOrigin(origin); >>> filter -> ChangeOriginOn(); >>> filter -> UpdateOutputInformation(); >>> filter -> Update(); >>> return filter->GetOut

Re: [Rtk-users] CUDA Ramp filter

Hi, I recently added the --subsetsize option (see this commit ). You can try "--subsetsize 1" instead of using rtksubselect. Simon On 15/06/2016 11:02, Cyril Mory wrote: Hi Shiras, Another user had the

Re: [Rtk-users] Fwd: About the newspacing flag

gt; projections from P1.mha to P2.mha, besides, i need change flag newspacing >>>> from 1 to 2. both of the results from RTK are pretty good. >>>> my questions are: >>>> 1) can i just regard the newspacing as the upsample operation with >>>> near

Re: [Rtk-users] .tiff Io estimation

Hi, This is correct but note that I have pushed tonight a change to allow float tif. Float images are handled as if you were passing the line integral directly. Simon On Fri, Apr 1, 2016 at 2:27 PM, Chao Wu wrote: > Hi Danny, > > Tiff follows the path of "ushort" in the

Re: [Rtk-users] scanner development problems

. Regards, Simon On Thu, Mar 17, 2016 at 4:23 AM, Vasiliy Nabokov <nabokajeleb...@gmail.com> wrote: > Dear Simon, as i understand --neworigin is origin for projections. my > projection's width 2452 and spacing 0.0148, so 2451/-2*0.0148=-18.137 > > On Wed, Mar 16, 2016 at 6:45 PM

Re: [Rtk-users] Python Wrapping

d in CUDA: is it the conjugate gradient or SART ? I have noticed that they are not wrapped at all, any guide on how to introduce new filters? Once I have tested my wrapping, I will submit a github pull-request. Thanks, Johnson *From:*simon@gmail.com [mailto:simon@gmail.com] *On B

Re: [Rtk-users] scanner development problems

process better, isn't it ? On Fri, Mar 18, 2016 at 1:27 PM, Simon Rit <simon@creatis.insa-lyon.fr <mailto:simon@creatis.insa-lyon.fr>> wrote: Ok, sorry, I erroneously mixed the size of the reconstructed volume and the size of the projections. Then your calculati

Re: [Rtk-users] Python Wrapping

17, 2016 9:23 AM > *To:* rtk-users@public.kitware.com; Simon Rit > *Subject:* [Rtk-users] Python Wrapping > > > > Hello, > > I am using the Python wrapped version of RTK. I have a question regarding > the wrapping: > > It seems that not all functionality is ava

Re: [Rtk-users] RTK with curved detector projection images

Hi, Not at present. We are working on this but this has not been released. Soon although I won't give a date because things have been delayed. Simon ___ Rtk-users mailing list Rtk-users@public.kitware.com

Re: [Rtk-users] Reconstruction Volume.

Hi, The typical solution (e.g., in clincial scanners) is to reconstruct the field-of-view of the scanner (every point in space that is seen by all source positions) because you know this is the only area of space where your reconstruction is going to be accurate. rtkfieldofview generates this FOV.

Re: [Rtk-users] Help Regarding FDK reconstruction

Dear Amjad, I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid? Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to

Re: [Rtk-users] How to define RTK geometry?

Hi, Can you share a dataset to make some quick tests? It's easier than a ping pong with several tests. Simon On Thu, Jul 21, 2016 at 11:45 AM, Данила Кожевников wrote: > Dears, > > I need help, I am new to RTK and now trying to reconstruct my data. For this > I write simple

Re: [Rtk-users] Issue with Cuda filter

Hi, The two algorithms differ: Cuda uses trilinear interpolation where Joseph uses bilinear interpolation in the slices of the main direction. Other than that, you should get very similar results (visually) from the same input images and geometry. Don't hesitate to share the dataset if you'd like

Re: [Rtk-users] Fwd: Have you encountered this artifact?

__ > > Andreas Gravgaard Andersen > > Department of Oncology, > > Aarhus University Hospital > > Nørrebrogade 44, > > 8000, Aarhus C > > Mail: andre...@phys.au.dk > > Cell: +45 3165 8140 > > > > 20

Re: [Rtk-users] Fwd: Have you encountered this artifact?

two projection stack files and two geometry files, >> then compare the projection stack files by subtracting one to the other >> (with SimpleRTK or clitk) and the geometry files with diff. If they are >> identical, then I do not see any reason why the reconstructions should b

Re: [Rtk-users] Contribute to RTK?

Hi Andy, Thanks, always good to hear that this is useful to some. Of course your dev are interesting to other, particularly a new recon algorithm. The best way to contribute is to do a fork on github (like other people, see this page ) and to

Re: [Rtk-users] Geometric calibration

the height? > > Which distance was known in your example? From the code it looks like the > distance to the rotation axis? > > Sepp > > On 22 Nov 2016, at 08.01, Simon Rit <simon@creatis.insa-lyon.fr> > wrote: > > Hi Sepp, > I did do a calibration script on a mi

Re: [Rtk-users] Fwd: Have you encountered this artifact?

Dear Andreas, Today we had the RTK training and some users were looking for a XIM file reader. I pointed to your contributions but any chance to have it put in RTK soon? Thanks in advance, Simon On Mon, Sep 19, 2016 at 9:26 AM, Simon Rit <simon@creatis.insa-lyon.fr> wrote: > Hi,

Re: [Rtk-users] Geometric calibration

Hi Sepp, I did do a calibration script on a micro CT platform. The idea was that I had a bb taken from 4 different view points at 4 different heights with a known distance. Their projected position was segmented beforehand on the projections and I tried to match the projections by optimizing the

Re: [Rtk-users] RTK simulated geometry BrainLab ExacTrac

Hi, Yes ! I have actually added that functionality recently from Thibault Notargiacomo's code see bool rtk::ThreeDCircularProjectionGeometry::AddProjection ( const HomogeneousProjectionMatrixType & pMat)

Re: [Rtk-users] Curved detector

Dear all, Apologies, this email has been sent by mistake to the RTK mailing list. Please ignore and delete it. Thanks, Simon On Mon, Dec 5, 2016 at 8:07 AM, Simon Rit <simon@creatis.insa-lyon.fr> wrote: > Beaucoup mieux je pense. > - page 1 : recalage non-rigide 3D/3D ? Tu veu

Re: [Rtk-users] Fwd: Have you encountered this artifact?

e in there.. > > Best regards > Andreas > > > __ > > Andreas Gravgaard Andersen > > Department of Oncology, > > Aarhus University Hospital > > Nørrebrogade 44, > > 8000, Aarhus C > > Mail: andre...@phys.au.dk >

Re: [Rtk-users] About CR(Computed Radiography)

Hi, If you mean Digitally Reconstructed Radiograph (DRR), this is what is called forward projection in RTK. See e.g. http://wiki.openrtk.org/index.php/RTK/Scripts/ForwardProjection Simon On Fri, Mar 24, 2017 at 9:54 AM, Cyril Mory wrote: > Hi Sam, > > > I think

Re: [Rtk-users] using rtk in matlab : input images for filters from matlab data types

n SimpleRTK > JosephForwardProjectionImageFilter_Execute: > $RTK_BUILD$/SimpleRTK-build/Code/BasicFilters/src/srtkJosephForwardProjectionImageFilter.cxx:100: > srtk::ERROR: Image2 for JosephForwardProjectionImageFilter doesnt match type > or dimension! > > I tried different

Re: [Rtk-users] iterative fdk

Hi, I would suggest to look at part V.3 of Cyril's thesis where he gives a brief description and provides a few references. Simon On Sun, Mar 26, 2017 at 1:37 PM, Robert Calliess wrote: > Hello, > > Would you

Re: [Rtk-users] using rtk in matlab : input images for filters from matlab data types

Hi Julia, I would have used volume = py.GetImageFromArray(result) instead of your last line. Does this work? If it does, then you have to be sure that you set correctly the origin, spacing and direction (the ITK meta information). One way to do this if you already have an image with the correct

Re: [Rtk-users] RTK data

Hi, Please use the mailing list. The Elekta reconstruction is in the archive elekta/img_1.3.46.423632.135428.1351013645.166/Reconstruction/1.3.46.423632.135428.1351013331.163.23.10.2012193405890.SCAN You can open it with, e.g., vv . The Varian reconstruction is in

Re: [Rtk-users] RTK-user

Hi, GetImageFromArray seems to be the good solution. Can you give the code that doesn't work (instead of copy pasting what works from the wiki)? Simon On Sun, Apr 16, 2017 at 10:27 PM, sare Borhani wrote: > Dear RTK.User, > > I'm using python wrapped version of RTK. > >

Re: [Rtk-users] I0EstimationProjectionFilter

ToAttenuationImageFilter::BeforeThreadedGenerateData(). > I tried to solve it using typename, but it seems to be unsuccessful. Could > you please have a look? The I0EstimationProjectionFilter seems to work now. > > Lotte > > > On 04-03-17 11:25, Simon Rit wrote: > > Hi Lotte, > This code h

Re: [Rtk-users] get simpleRTK image from array

Hi, You need to work with numpy, as explained in the help: >>> import SimpleRTK as srtk >>> help(srtk.GetImageFromArray) Help on function GetImageFromArray in module SimpleRTK.SimpleRTK: GetImageFromArray(arr, isVector=False) Get a SimpleRTK Image from a numpy array. If isVector is True,

Re: [Rtk-users] Obtaining Cone Beam projections using sRTK

t3 = str(Disp2[l,1,t]) > t4 = str(Inplaneshiftsx_new[l,t]) > t5 = str(Inplaneshiftsy_new[l,t]) > t6 = str(shiftsx2_new[l,t]) > t7 = str(shiftsy2_new[l,t]) > t8 = str(shiftsz2_new[l,t]) >

Re: [Rtk-users] Obtaining Cone Beam projections using sRTK

Hi, Please use the mailing list. A 1 mm shift of an object at the isocenter should indeed translate in a 1.536 mm shift on the projection with the defined geometry. I don't see anything wrong in your code but you have only provided a part of it. Could you provide a full self-contained script?

Re: [Rtk-users] get simpleRTK image from array

rom? > > Best regards, > Sareh > > On Tue, Apr 18, 2017 at 1:31 PM, Simon Rit <simon@creatis.insa-lyon.fr > > wrote: > >> Hi, >> You need to work with numpy, as explained in the help: >> >> >>> import SimpleRTK as srtk >> >>>

Re: [Rtk-users] Reconstructing from fan-beam projections

rements. What is exactly needed? And is it > similar for the ADMM wavelet reconstruction? > > > > Best regards, > > > > Jacob > > *From:* simon....@gmail.com [mailto:simon@gmail.com] *On Behalf Of *Simon > Rit > *Sent:* 17. maj 2017 16:42 > > *To:* Jacob

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

Re: [Rtk-users] Reconstructing from fan-beam projections

s 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@gmail.com [mailto:simon@gmail.com]

Re: [Rtk-users] Forward and Back projections in 3D parallel geometry

Hi Yannick, Yes, that's correct. It should not be too difficult to implement, at least on the CPU, now that we have iterators with the geometry , but I still haven't done it. In practice, I do a pseudo

Re: [Rtk-users] On the fly CBCT reconstruction

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

Re: [Rtk-users] Reconstructing from fan-beam projections

> Jacob > > > > *From:* simon@gmail.com [mailto:simon@gmail.com] *On Behalf Of *Simon > Rit > *Sent:* 16. maj 2017 14:54 > *To:* Jacob Frøsig <j...@force.dk> > *Cc:* rtk-us...@openrtk.org > > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections

Re: [Rtk-users] Reconstructing from fan-beam projections

s, > > > > Jacob > > > > > > *From:* Rtk-users [mailto:rtk-users-boun...@public.kitware.com] *On > Behalf Of *Simon Rit > *Sent:* 15. maj 2017 17:32 > *To:* rtk-us...@openrtk.org > > *Subject:* Re: [Rtk-users] Reconstructing from fan-beam projections >

Re: [Rtk-users] SIRT Reconstruction

Dear Lotte, Thanks for the data. I have had a look (you can thank Ana for the reminder). The snapshots show indeed a bad result. My advice is to work on a small example first, as the one enclosed for this test (you can create one from real data to). Since I have never worked with SIRT before, I

Re: [Rtk-users] SIRT Reconstruction

Thanks for the reminder. See: https://public.kitware.com/pipermail/rtk-users/2017-September/010481.html On Wed, Aug 30, 2017 at 11:46 AM, ana wrote: > Hi, > > I was wondering if you guys had the opportunity to look into SIRT > reconstruction. > There was a thread on this

Re: [Rtk-users] RTK compilation error

Hi, I don't know and I don't think it's an RTK problem. I would try adding -lpthread to the CMAKE_EXE_LINKER_FLAGS in ccmake. Best regards, Simon On Mon, Oct 9, 2017 at 7:20 PM, Giovanni Di Domenico wrote: > HI, > > I have tried to compile RTK, but the following error

Re: [Rtk-users] Hounsfield Calibration for CBCT .

Hi, I am not sure I understand your question but it seems to me that your problem is beam hardening. It is a known limitation of polychromatic x-ray imaging and there is a wealth of literature on the subject. Best regards, Simon On Mon, Oct 9, 2017 at 10:23 AM, M B Sai Mahesh <

Re: [Rtk-users] About geometric correction！

Dear M.K., This is difficult. We have made some works in this direction http://www.creatis.insa-lyon.fr/~srit/biblio/lesaint2017.pdf but the (Python) code cannot be easily shared. If you can, I would suggest to redo the acquisition if possible... Best regards, Simon On Mon, Nov 13, 2017 at 3:22

Re: [Rtk-users] FDK for planar ct

gt; the object is moving on a circular path. There are arrows between the > different detector positions showing the > > moving direction. The source is static. > > > > Kind regards, > > Robert > > > > *Gesendet:* Dienstag, 24. Oktober 2017 um 16:47 Uhr > *Von:* &q

Re: [Rtk-users] Error Issues about Building RTK

Dear Daniel, Please send your questions to the mailing list. Regarding FFTW: yes, RTK works without FFTW. It then uses the (slow) implementation of the FFT in ITK. I know that some vendors use RTK without FFTW but with CUDA to enable fast reconstruction. There is one piece of software that won't

Re: [Rtk-users] Reconstruction filter progress observer

Dear Albert, We have not implemented anything in this direction so far. But it would be useful to have it and I know there is a mechanism to do that in ITK Have you ever used it on your side? I think the idea is: - in the reconstruction filter, to create and regularly call a ProgressReporter

Re: [Rtk-users] FDK for planar ct

the picture, the object is moving on a > circular path but not rotating around the > center point (red cross in the image). > > > Kind regards, > Robert C. > > *Gesendet:* Donnerstag, 12. Oktober 2017 um 07:14 Uhr > *Von:* "Simon Rit" <simon@creatis.insa-lyon.fr&

Re: [Rtk-users] rtkfdk and rtksart application input projection type and voxel value range

Hi, Be aware that since the "object scanned always occupies the entire projection" you are dealing with the (difficult) interior problem. See, e.g., http://doi.org/10.1109/MSP.2010.936743. It's not surprising for this problem that FDK and SART give different answers. Best regards, Simon On Fri,

Re: [Rtk-users] Simple FDK reconstruction using SimpleRTK does not work

Dear Mathis, Sorry to hear about your difficulties. You use AddProjection with a matrix which, internally, converts your projection matrix to parameters that are used in the FDK reconstruction. After writing down the produced geometry, it turns out that you rotate around Z where RTK works in FDK

Re: [Rtk-users] rtkThreeDCircularProjectionGeometry cannot be cloned

ned and the converter will reflect the object as it > was when it was set, regardless of any changes done to it by the caller. > > Actually, I think I can do with behavior 1. However, as it is now, I don't > think I have possibility to implement behavior 2 at all. > > Best reg

Re: [Rtk-users] rtk user : FDKConeBeamReconstructionFilter

ume in a 2x2x2 finner grid and then > perform a 2x2x2 binning to the output, if the voxel size is about 2 times > of the pixel size. Despite that the amount of computation is 8 times > higher, is there any obvious benefit (resolution, contrast, S/N etc.) under > this scheme? > > Be

Re: [Rtk-users] rtk user : FDKConeBeamReconstructionFilter

Hi Elena, Please post your questions to the mailing list, they can interest everyone in the community and you may get (better) answers before mine. FDK is very simple: it takes the projections, weight them with the cosine + angular gaps, apply the ramp filter with a kernel adapted to the number of

Re: [Rtk-users] Problems with --like and --dimension parameters of rtkforwardprojections and rtkfdk

Hi Anais, It's a bit hard to check what's going on without the command lines. Can you try to send the command lines that give you some problems, e.g. based on the forwardprojection example? Thanks, Simon On Mon, Jan 29, 2018 at 12:03 PM, wrote: > Hi, > > My

Re: [Rtk-users] CUDA Forward Projection Intensity Variance with Geometry Shift

Hi Daniel, I don't see how moving the source and the detector could trigger a drastic drop in intensities. If you can send two geometry files (before and after the drop), we can try to have a look. Best regards, Simon On Sun, Feb 11, 2018 at 8:18 AM, Daniel Xun Lin wrote:

Re: [Rtk-users] Reducing the pattern of errors

Hi, These are numerical errors. How did you create the projections? It seems that you have used the voxelized phantom to simulate the projections. This enhances strongly these artefacts. This is why most people compute simulated projections analytically with simple analytical shapes (as the Shepp

Re: [Rtk-users] RTK Scatter Correction

Dear Lotte, These two options address different issues. The first one deals with the patient scatter and the second one with the detector glare which might come from the detector scatter (but maybe not (only)). See the work of, e.g., Poludniowski to understand the difference

[Rtk-users] Release of RTK v1.4.0

Joshi, Lotte Schyns, Lucas Gandel, Sébastien Brousmiche, Simon Rit, Thibault Notargiacomo and Thomas Baudier. As usual, be aware that we don't focus on releases since we have a public github repository <http://github.com/SimonRit/RTK> that we try to keep stable. I still recommend the use

Re: [Rtk-users] Online reconstruction

Hi, Yes, you can even if you don't know the geometry in advance. The application rtkinlinefdk and its code rtkinlinefdk.cxx illustrates this. Best regards, Simon On Thu, Feb 22, 2018 at 2:05 PM, Chao Wu wrote: > Hi Fredrik, If the geometry and projection angles are known in

Re: [Rtk-users] problem while determining the interpolation weights in 4D ROOSTER Reconstruction

Hi, If you look at the code , you'll see that the error message corresponds to the case where you have a phase which equals the number of frames. This cannot be since it is 0-based. In other words, with the

Re: [Rtk-users] problem while determining the interpolation weights in 4D ROOSTER Reconstruction

; Thanks. > > Regards > > Ruoyan Meng > On 12/26/2017 17:14，Simon Rit<simon@creatis.insa-lyon.fr> > <simon@creatis.insa-lyon.fr> wrote： > > Hi, > If you look at the code > <https://github.com/SimonRit/RTK/blob/master/code/rtkPhasesToInterpolation

Re: [Rtk-users] RTK + Cuda 9 + gcc 6.4 segfaults

pploganphantomtest > - rtkwaveletstest > - rtkargsinfomanagertest > > Kind regards > Mathis Hoffmann > > On Do, Dez 21, 2017 at 3:50 PM, Simon Rit <simon@creatis.insa-lyon.fr> > wrote: > > Hi, > Thanks for the report. Seems like something is happening in the ITK

Re: [Rtk-users] RTK + Cuda 9 + gcc 6.4 segfaults

Hi, Thanks for the report. Seems like something is happening in the ITK code. Are other non cuda tests failing? Did you also compile ITK with C++11? BTW, why is it required? Best regards, Simon On Thu, Dec 21, 2017 at 3:20 PM, Mathis Hoffmann wrote: > Hello, > > I was

Re: [Rtk-users] SimpleRTK : help for defining a correct json file for CudaBackProjectionImageFilter

Hi Yannick, I would just try to change the step size . Indeed, the CPU version is the Joseph projector and it adapts automatically the step size to each ray for bilinear

Re: [Rtk-users] SimpleRTK : help for defining a correct json file for CudaBackProjectionImageFilter

e to the > voxel size then (if I understand well). It seems that the implementation of > the CudaBackProjectionImageFilter doesn't use any stepsize. I'll let you > know. > > Merry Christmas to you, > Yannick > > Le 22/12/2017 à 22:55, Simon Rit a écrit : > > Hi Yannick,

Re: [Rtk-users] SimpleRTK : help for defining a correct json file for CudaBackProjectionImageFilter

the SetStepSize() function through > SimpleRTK. Is it normal ? Does it come from the .json file or the template ? > > Thanks in advance. > Yannick > > Le 22/12/2017 à 23:34, Simon Rit a écrit : > > No it doesn't, it's voxel based. The adjoint w

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

Hi, It's not clear to me how you came up with your source_y value. Assuming that the origin of your projections is 0,0,0, I would advise to set the geometry with --proj_iso_x=202.3 --proj_iso_y=202.3 (or, equivalently, set a new origin to the projection equal to -202.3,-202.3,0). The --arc value

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

ationMatrix( > ComputeTranslationHomogeneousMatrix(sourceOffsetX-projOffsetX, > sourceOffsetY-projOffsetY) ) also supports that they are projection origin > wrt isocenter instead of isocenter wrt projection origin. > > Best regards, > Chao > > > Simon Rit 于2018年8月21日周二 下午1:26写道： &g

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

ot; is much less ambiguous. > Maybe instead of saying "... (and not to m_Origin in ITK)", you can write > down the actual relationship, something like >In the following, origin refers to point with coordinates 0 mm. In ITK > this is at Pixel(0,0)−m_Origin in 2D or Voxel(0,

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

lues to the two arguments since > "the coordinates of isocenter in the projection image coordinate system" > are positive. > > I did not suggest the redundance. I meant the way how the tranlation is > calculated (source_# - proj_iso_#) proves that proj_iso_# is projection > ori

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

mple=-16.412937. My understanding is that this should > be the SourceOfsetY. However, in my first attempt today, I didn't use that > argument. > > Many thanks for helping me. > > Best Regards, > Milan > > > > Am 21.08.2018 um 13:25 schrieb Simon Rit: > > Hi, &

Re: [Rtk-users] GPUs testing

6 >> 0.0484766 >> ProjectionsReader 1 1 >> 44.7685 >> Self 129 129 >> 0.0506474 >> StreamingImageFilter 2 2 27.713 >> >> VarianOb

Re: [Rtk-users] Cannot account for too large detector displacements, a part of space must be covered by all projections.

Hi, I checked and it works like a charm for me. If you check your output, you'll see that it says that it found 0 file. It should find 669. Maybe there is a problem with the single quotes around .*.his? Try to remove them? You actually just pass his without quotes, it will then search all files

Re: [Rtk-users] rtk compile error: can not open file rtkcuda.lib

Hi, Is this using the current HEAD? There was yesterday a commit that might help: https://github.com/SimonRit/RTK/commit/0a2d4d573ab7bcf028c1f63d1dd417db29aa8a04 Otherwise, I'm not sure what's wrong. Best regards, Simon On Tue, Sep 11, 2018 at 10:18 AM YusiCHEN wrote: > hi rtk user, > > > I

Re: [Rtk-users] z - resolution ?

Helllo Robert, In RTK, the rotation axis is by default y so slice thickness would be y resolution. I would indeed chose the v pixel spacing at the center of rotation for the y direction spacing. For x and z (axial slice) pixel spacing, it depends on both the detector pixel spacing in the u pixel

Re: [Rtk-users] More errors with 360 projections than 180 for SART

Hi Anais, The suggestion posted by Chao might be helpful to improve both results. My intuition is that this is caused by the fact that SART has no regularization and it is know that it will start to diverge from the solution after a few iterations. Setting the number of iteration is a way of

[Rtk-users] ATTIRE summer school

ion (schedule, program, prices...) on https://attire.sciencesconf.org. Note the (optional) hands-on sessions using RTK. We are looking forward to seeing you in Yenne, The ATTIRE Team (Rolf Clackdoyle, Michel Defrise, Laurent Desbat, Jérôme Lesaint, Frédéric Noo, Simon

Re: [Rtk-users] compilation issues in case of outside of ITK directory build

for target > 'applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/all' > failed > make[1]: *** > [applications/rtkamsterdamshroud/CMakeFiles/rtkamsterdamshroud.dir/all] > Error 2 > Makefile:129: recipe for target 'all' failed > make: *** [all] Error 2 > > On

Re: [Rtk-users] compilation issues in case of outside of ITK directory build

.3.0 20170406 (Ubuntu 6.3.0-12ubuntu2) > cmake version 3.13.0-rc1 > > > > > On Fri, Oct 26, 2018 at 8:05 PM Simon Rit > wrote: > >> Hi, >> Are you sure it's shared with the same compilation mode (Debug or >> Release) ? >> Simon >> >> O

Re: [Rtk-users] compilation issues in case of outside of ITK directory build

Hi, It seems that you are trying to compile against an installed ITK_DIR. This is no longer possible, see this thread: https://github.com/SimonRit/RTK/issues/207 Can you try to compile against your build directory (set ITK_DIR to the build directory)? Thanks, Simon On Thu, Oct 25, 2018 at 5:16 PM

Re: [Rtk-users] Physical interpretation of the input and output images when doing a forward projection

Hi Estelle, Forward projection simply takes the line integrals of your volume. So 3D images have to represent the physical quantity you want to integrate. For x-ray imaging, you generally want to have linear attenuation coefficient. But for PET or SPECT, that would be the emission map in counts

Re: [Rtk-users] ATTIRE summer school

Dear all, Just a quick reminder that the cheapest price for the summer school I co-organize is valid until the end of December. Don't forget to register! Best regards, Simon On Mon, Oct 15, 2018 at 11:56 AM Simon Rit wrote: > Dear RTK users, > We are proud to announce the first e

Re: [Rtk-users] compilation issues in case of outside of ITK directory build

Hi, Sorry for the long delay. I couldn't resolve the problem but Matt McCormick did it for us: https://discourse.itk.org/t/link-issue-with-dynamic-libraries/1434/2 That fixed the issue for me. Best regards, Simon On Wed, Oct 31, 2018 at 4:55 PM Simon Rit wrote: > Hi, > I can rep

Re: [Rtk-users] Running the WaterPreCorrection Example

Hi, Have you checked that it's not in a subfolder? I remember that it got in a subfolder for some versions. To be honest, we are not using SimpleRTK anymore, we are gradually switching to a python package for RTK as an external module of ITK. I will update the examples when we release it. Best

Re: [Rtk-users] RTK for Python : installation failed

Hi Yannick, It's weird, it's trying to compile the package and I have no idea why. Are you on a 32-bit machine? It may be the cause, there is no pre-compiled version for (old) 32-bit Windows. Since it's an ITK problem, I think the best is to ask the specialists on http://discourse.itk.org/. Simon

Re: [Rtk-users] RTK for Python : installation failed

K. > > Regards, > > Yannick > > > > > > *De :* Simon Rit [mailto:simon@creatis.insa-lyon.fr] > *Envoyé :* mardi 2 avril 2019 09:07 > *À :* Yannick Grondin > *Cc :* rtk-users > *Objet :* Re: [Rtk-users] RTK for Python : installation failed > > > >

Re: [Rtk-users] Cannot download ExternalData during build (RTK 2.0)

Hi, This is strange, I'm guessing a temp issue with data.kitware.com. Now, the link https://data.kitware.com/api/v1/file/hashsum/SHA512/315f410d858da64079b587826c5e8668c3ec0c41fc59a4c68a0f183d1678a89c6b240e39e1fbccdc0cedda20d53234f0c67761dfa7e04608009b44deee175dff/download works. Can you try

Re: [Rtk-users] GPU kernel do not change output variables

Hi, Sounds like a challenge. When you say you set fixed numbers, did you check that you reach the point where you set this number? You can use cuprintf to check what's going on in the kernel. One thing wrong I noticed: you use size.Fill in a loop, which is a bit odd because it will Fill the size

Re: [Rtk-users] GPU kernel do not change output variables

t;cudaMemcpy(dev_out_y, dev_grad_y, outputMemorySize, > cudaMemcpyDeviceToHost); > >CUDA_CHECK_ERROR; > >cudaMemcpy(dev_out_z, dev_grad_z, outputMemorySize, > cudaMemcpyDeviceToHost); > >CUDA_CHECK_ERROR; > > } > > > > I am not sure if this viola

Re: [Rtk-users] rtk::CudaVectorImage available

the memory is reorganized in the rtk::CudaImageFilter to make > it more efficient on the GPU (like a new image for each vector component). > Or it is handled in a different way? > > > > I think it will be more time consuming and error prone to do it by myself > since I am not very

Re: [Rtk-users] segfault in RTK 2.0

Hi, Thanks for sharing your experience. I tried to use your code to reproduce your problem but I couldn't. Enclosed is the code that I run with import daye simulator = daye.simulator() simulator.runCBCT('proj.mha', 0, 0) simulator.buildVolumeFromFile('proj.mha','recon.mha',simulator) Does it

Re: [Rtk-users] Regarding rtk::ProjectionsReader

Dear Amarnath, GenerateData exists, see http://www.openrtk.org/Doxygen/classrtk_1_1ProjectionsReader-members.html This is ITK's internal machinery. When you call Update, it will call itk::DataObject::Update(). This will call UpdateOutputInformation, PropagateRequestedRegion and UpdateOutputData.

Re: [Rtk-users] cast itk:::Image to itk::CudaImage

ke rtkfdk with > gpu on without any problem though, > By the way I am using CUDA 9.2.88. > > Tao > > > > > > Simon Rit 於 2019年1月30日 週三 上午1:25寫道： > >> Hi, >> No, not really. In my experience, this occurs mainly when you don't have >> a GPU properly conf

Re: [Rtk-users] RTK Books

Hi, No, all we have is the wiki and the doxygen documentation. Simon On Mon, Apr 29, 2019 at 10:07 AM Ali ghorbanian wrote: > Hi, > Have a book for more explanations in libraries and implemented functions > in the RTK? >

Re: [Rtk-users] Use existing Images when copying from/to GPU

r/utilities/ITKCudaCommon/include/itkCudaImage.h#L32> > . > You can always ask explicit transfers by calling the functions of the data manager (accessible via CudaImage::GetCudaDataManager()) > > > Best > Clemens > > Am Mo., 8. Juli 2019 um 16:20 Uhr schrieb Simon Rit <

Re: [Rtk-users] ConjugateGradientConeBeamReconstructionFilter

Hi, The conjugate gradient algorithm solves weighted least squares. If you want to use unweighted least squares, simply pass an image filled with ones which has the same size as the projections. Simon On Sat, Jul 13, 2019 at 8:01 AM Ali ghorbanian wrote: > Hi, > I read the projections of a fan

Re: [Rtk-users] Use RTK library for fan beam CT

rrore(use CudaFDKConeBeamReconstructionFilter method for Reconstruction) > voxel-based FDK back projector can currently not handle Cylindrical > Detectors. > So I can not use the FDK filter? > Which filter should I use for RadiusCylindricalDetector in RTK? > > Best regards > > On Mon,

Re: [Rtk-users] Use RTK library for fan beam CT

Hi, RTK only works in 3D. Still, you can describe this in 3D. You must set RadiusCylindricalDetector. See the geometry doc here . Note that only iterative reconstruction currently works with this geometry. Simon On Sun, Jun 30, 2019 at 2:06 PM Ali

Re: [Rtk-users] GPU support of PyPI package

Hi, No yet! We aim at proposing this soon but it's not ready. The best practice is to build from ITK, turn on Module_RTK, RTK_USE_CUDA and ITK_WRAP_PYTHON. Someone has already requested a proper compilation doc, we'll work on it asap, sorry for the inconvenience. Simon On Tue, Jul 2, 2019 at 5:51

  1   2   3   >