Re: [Rtk-users] bWithExternalHalfPixelBorder in RayBoxIntersectionImageFilter

Dear Chao, Thanks for the question and sorry for the delay in answering it. The boolean allows to determine if the box goes from itk::Image::Origin to the coordinate of the last pixel or whether you want to add a half voxel border, see code here

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

using this >> commit >> <https://github.com/SimonRit/RTK/commit/99a6626f42e6654d11a780127610c95d3c1a063e> >> and >> am wondering what's the best pratice to install it. >> >> >> Thank you very much >> Clemens >> >> On Wed,

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

> <https://github.com/SimonRit/RTK/blob/master/examples/FirstReconstruction/FirstCudaReconstruction.py#L64-L70>. >> For the output projections, I use an ImageView from a numpy.zeros array >> with according shape, spacing and origin and transfer that to GPU the same >> way. I t

Re: [Rtk-users] WaterPreCorrectionFilter Example - Python

Hi, Apologies for not working on this before. I have updated the wiki page with the code adapted to the new wrapping. Look at the diff between the 2 versions to see the necessary modifications with the new wrappings. I hope this (still) helps, Simon On Wed, Feb 13, 2019 at 8:03 AM Amarnath S

Re: [Rtk-users] Half Fan dataset

on achieved with the > exotic geometry :^] and the xml I generated for it (beware that my detector > is 298 mm wide and the displacement is of +/-120 mm) > > Best regards, > Gabriele > > > > *Da:* Simon Rit > *Inviato:* martedì 29 ottobre 2019 18.21 > *A:* gabriele.belotti.ber

Re: [Rtk-users] Is it possible to install RTK in Windows?

Hi, Please use the mailing list. This should work. Which version of python are you using? The packages are currently compiled for python 3.5, 3.6 and 3.7, see here . Best regards, Simon On Thu, Nov 7, 2019 at 8:22 AM jay chen wrote: > Dear Simon: >

Re: [Rtk-users] RTK crashes silently when calling Update in Python

Hi, Thanks for reporting, I guess you can open an issue on github. Can you try to see if it works better with 3D images (CPUImageType = rtk.Image[itk.F,3])? We mainly use the projections reader to load a stack of projections. If not, can you share your projection? Best regards, Simon On Thu, Nov

Re: [Rtk-users] RTK crashes silently when calling Update in Python

ied with 3D images as well, however it gives the same result. I > have attached one similar projection to this mail. > > Best regards, > Christian > > Den tor. 21. nov. 2019 kl. 12.05 skrev Simon Rit < > simon@creatis.insa-lyon.fr>: > >> Hi, >> Thanks

Re: [Rtk-users] Reconstruction artefact with SART

M > https://ibb.co/MnMk5Ny > https://ibb.co/gzfPQG1 > > So I think that adding the step size option in rtksart should get rid of > my problem, but I would like your feedback before, as I trust your > experience more than my intuition :) ! > > Thanks again, > > Vincent

Re: [Rtk-users] Multi GPU capabilities

Hi, No. This is quite a challenge to implement this and we have no resources on this topic. My first attempt to do this would be to use ASTRA from RTK. RTK only automagically select the "best" GPU, see here

Re: [Rtk-users] Reconstruction artefact with SART

, 2019 at 6:19 PM vincent wrote: > Hi Simon, > > well the step size marginally improved the result. But using > CudaVoxelBased as the BP rather than CudaRayCast completely solved it ! > > Thank you for your time and advice, > > best regards, > > Vincent > On 27.10.

Re: [Rtk-users] Half Fan dataset

ed on this? (two rotations/acquistion given two opposite > detector displacements) > > Thanks in advance, > Gabriele > > > > > > > > *Da:* Simon Rit > *Inviato:* venerdì 11 ottobre 2019 13.10 > *A:* gabriele.belotti.berg...@gmail.com > *Cc:* rtk-users &

Re: [Rtk-users] Reconstruction artefact with SART

Hi Vincent, There is a problem indeed! It's hard to guess what's the problem from the images you sent. I would check the projections to see what could be wrong. The first thing I would check for example is whether air is really at 0 (as it should be). You can also look at the difference between

Re: [Rtk-users] HNC reader

Hi, I think there's been a confusion on my side when writing the release notes of RTK 1.4. I merged a pull request from Andreas Gravgaard who implemented the Xim reader based on the Hnc reader. There is a commit

Re: [Rtk-users] HNC reader

nks Simon! > I’m able to retrieve those codes for a start and that’s good! Currently > I’m using 1.4.0 so I don’t have to fiddle around too much. > How would you go for making the bzip2 dependency optional? Maybe creating > an option flag in CMake and editing the reader accordingly? > Gabr

Re: [Rtk-users] Half Fan dataset

Hi, It's easy to generate, you need to offset your detector, either via the RTK geometry or by setting the first coordinate of the origin of your projection to something which makes the projection uncentered. For example, in the geometry : rtksimulatedgeometry -n 180 --proj_iso_x 100 -o g

Re: [Rtk-users] Offset detector with ADMM - hole in centre

Hi, I don't have much experience with ADMM. However, in my experience with the conjugate gradient algorithm, it's worth weighting the least squares cost function with the redundancies at the center. This has been documented by others, see e.g. https://doi.org/10.1088/0031-9155/58/2/205 This seems

Re: [Rtk-users] Blurred piece-wise reconstruction

Simon Rit <mailto:simon@creatis.insa-lyon.fr>> 于2020年2月12日周三 上午9:28写道： Actually, the way I have implemented the streaming, it still allocates the 30Go complete volume and compute it piece by piece. One thing you could try is to remove the streamerBP object, connect

Re: [Rtk-users] Blurred piece-wise reconstruction

, but to no avail. > > I'll investigate further tomorrow. > > Thank you again for your help, > > Vincent > On 2020-02-11 8:08 p.m., Simon Rit wrote: > > Have you tried the combination of both? To be clear, --divisions acts on > the reconstructed volume so it should be ~

Re: [Rtk-users] Half Fan dataset

g the code, I’ll transfer the changes to a clone of the current > release and share it as soon as possible and we’ll look into optimizing it. > > Best wishes, > Gabriele > > > > *Da:* Simon Rit > *Inviato:* mercoledì 22 gennaio 2020 11.46 > *A:* gabriele.belotti.berg

Re: [Rtk-users] Blurred piece-wise reconstruction

am afraid I forgot to mention something in my last email. I tried to > use the lowmem option, as you suggested a while ago in the list for the > same problem, but I am afraid I am still getting the same error. > > kind regards, > > Vincent > On 11.02.20 17:36, Simon Rit wrote: &

Re: [Rtk-users] Half Fan dataset

you feel this feature could be merged into Rtk tree I would be > glad to open a pull request on git and dive more into details. > > Best regards, > Gabriele > > > > Da: Simon Rit > Inviato: giovedì 31 ottobre 2019 00.22 > A: gabriele.belotti.berg...@gmail.com > Cc:

Re: [Rtk-users] 3D CT scan to 2D DRR

Great! ___ Rtk-users mailing list Rtk-users@public.kitware.com https://public.kitware.com/mailman/listinfo/rtk-users

Re: [Rtk-users] fatal error LNK1104 and C1083

Hi, So ITK 5.1 has not been released yet. It seems that you're using the HEAD of the master branch? Because this has been fixed today (I hope), it's a change from ITK impacting RTK: https://github.com/SimonRit/RTK/commit/957d049eff68011723e9c6ff0e63fc404343f8fb Simon On Wed, Apr 15, 2020 at 11:15

Re: [Rtk-users] Rotation before and during rktprojections

Hi Vincent, Everything you did is correct but rtkfdk always applies the ramp filter along the first dimension and does not check if this corresponds to the direction orthogonal to the rotation axis. For your case, it is probably not so difficult to adapt the code. When there is a small rotation,

Re: [Rtk-users] fatal error LNK1104 and C1083

> just download and use the 5.0.1 stable release from itk.org/download? > > Henry > > On Wed, Apr 15, 2020 at 5:18 PM Simon Rit > wrote: > >> Hi, >> So ITK 5.1 has not been released yet. It seems that you're using the HEAD >> of the master branch? Because this ha

Re: [Rtk-users] 3D CT scan to 2D DRR

Hi, There can be two reasons: - you are working with unsigned short as input and output. This is tricky because you must be sure that your pixel values will cover the range between 0 and 255. For example, if your phantom has values between 0 and 1, conversion to unsigned short will blank it. I

Re: [Rtk-users] DRR image generation from 3D CT

Hi, Look at the doc on the geometry file and rtksimulatedgeometry for creating one file. AddProjection

Re: [Rtk-users] How to configure beam characteristics such as filtration

Hi, This is not possible in RTK, the forward projections are just the line integral of a given voxelized volume. In the Joseph forward projection , there is a number of templated functors that can be

Re: [Rtk-users] Converting 3D Image to 2d image

Hi, Yes, it should. Have you built the default ITK modules? If yes, I'm not sure what's going on but you can ask on itk discourse . Simon On Wed, Apr 1, 2020 at 7:53 PM Henry Cope wrote: > Good Afternoon, > > I'm currently trying to create a program to read a given 3D

Re: [Rtk-users] problem with installing RTK and Python

Hi Yannick, Sorry for the late reply. Actually, we do not have a python 3.8 itk-rtk release yet. That's probably the problem here... We'll try to provide one asap! Simon On Tue, Apr 21, 2020 at 6:09 PM Yannick Grondin < yannick.gron...@surgiqual-institute.com> wrote: > Hi all, > > I have a

Re: [Rtk-users] Forward Projection

Hi, ForwardProjectionImageFilter is a purely virtual class. Try for example Joseph's projector . The forward projectors in RTK need two inputs : empty projections in which to project (input 0) and the volume to

Re: [Rtk-users] problem with installing RTK and Python

d it depends on the new ITK 5.1 python package (which has not even been announced yet!). I hope this helps, Simon On Tue, Apr 28, 2020 at 5:17 PM Simon Rit wrote: > Hi Yannick, > Sorry for the late reply. Actually, we do not have a python 3.8 itk-rtk > release yet. That's probably the proble

Re: [Rtk-users] DRR image generation from 3D CT

Exception thrown at 0x00007FF68D387919 in FirstReconstruction.exe: >>> 0xC005: Access violation reading location 0x. >>> >>> I have attached the source code (.cpp) file for your further reference. >>> Please let me know if I have done any mist

Re: [Rtk-users] Rotation before and during rktprojections

t; right coefficients for an itkPermuteAxis filter. > > I don't think it is worthy to be included in the official source, but I am > happy to share if someone requires it. > > Best regards, > > Vincent > On 15.04.20 20:13, Simon Rit wrote: > > Hi Vincent, > Everything you did is cor

Re: [Rtk-users] DRR image generation from 3D CT

s)add_executable(FirstReconstruction FirstReconstruction.cpp > )#target_link_libraries(FirstReconstruction > ${RTK_LIBRARIES})target_link_libraries(FirstReconstruction > ${ITK_LIBRARIES})* > > On Wed, Apr 22, 2020 at 4:03 PM Simon Rit > wrote: > >> Hi, >> Can you check this

Re: [Rtk-users] Error in the FFTRampImpageFilter

ut()) > #weights.SetNumberOfWorkUnits(1) > #weights.InPlaceOff() > > ramp = rtk.FFTRampImageFilter[ImageType,ImageType,itk.D].New() > ramp.SetInput(sl.GetOutput()) > ramp.Update() > > > Le ven. 8 mai 2020 à 22:15, Simon Rit a > écrit : > >> Hi, >> I can

Re: [Rtk-users] 4D Phase-correlated Reconstruction

Hi, I think you should look at rtkfourdfdk which does what you want. rtk::SelectOneProjectionPerCycleImageFilter will select the projections for you. Can you try to reimplement this in Python? We'll help if

Re: [Rtk-users] 4D Phase-correlated Reconstruction

ubSelectImageFilter.html> > should have these set methods but I don’t know why I cannot use them on > Python. > > Sorry for these troubles. Hope to get your help. > > > > Best, > > Zhehao > > > > *From: *Simon Rit > *Sent: *Friday, May 15, 2020 4:21 AM

Re: [Rtk-users] Python Wrapping

Hi Jérôme, Not everything is wrapped in Python yet. To know if a filter should be wrapped, you can check if there is a corresponding file in the wrapping subdirectory. You can try to create one

Re: [Rtk-users] Python Wrapping

ly stupid question, but > quite a different game... > In other words, can I try on one file or should I first check all the > missing filters that I need to recompile only once. > > Thanks, > Jérome > > Le mar. 5 mai 2020 à 15:28, Simon Rit a > écrit : > >> Hi Jérôm

Re: [Rtk-users] Trouble on the FirstReconstruction example

Hi, Thanks for the report, I can reproduce the problem. Actually, ITK recently updated their packages and it seems that our old packages are not compatible with the new ones. We will release new ones soon but in the mean time, you should use an older version of ITK packages (5.0.1) or use a

Re: [Rtk-users] building FirstConstruction

Hi, This is a command line tool, run it from a shell and you'll get usage information. Simon On Mon, May 11, 2020 at 7:51 AM 나윤호 wrote: > I just found out that FirstReconstruction.exe immediately closes as soon > as I open it. > > why is this happening? > > > > 2020년 5월 11일 (월) 오후 1:50, 나윤호 님이

Re: [Rtk-users] what does ggo file do?

This is a parameter file for gengetopt which is a tool for parsing the command line. See here . GGO is a macro which groups a number of commands that are systematically applied to RTK command line tools. Simon On Mon, May 11, 2020 at 9:44 AM

Re: [Rtk-users] 4D Phase-correlated Reconstruction

ed data here( > https://drive.google.com/drive/folders/1SFXr4ehI1N8Wh0BAMlRqIah9cXwukRYJ ). > > > > > Thank you again. > > Zhehao > > > > > > *From: *Simon Rit > *Sent: *Wednesday, May 13, 2020 3:59 AM > *To: *Zhang, Zhehao > *Cc: *rtk-users@publi

Re: [Rtk-users] Error in the FFTRampImpageFilter

for dep in deps: > > ---> 83 LoadModule(dep, namespace) > > * 84* > > * 85* if itkConfig.ImportCallback: > > > ~/src/ITK-build/Wrapping/Generators/Python/itkBase.py in LoadModule(name, > namespace) > > * 81* deps = sorted(data['depends']) &

Re: [Rtk-users] 4D Phase-correlated Reconstruction

t; BTW, if I need to utilize more projections for each phase, is there some > integrated method in RTK to do so? Or you mean that I need to handle it by > myself? > > > > Best regards, > > Zhehao > > *From: *Simon Rit > *Sent: *Thursday, May 14, 2020 2:17 AM > *To:

Re: [Rtk-users] Add noise to projections

Hi, There is an AdditiveGaussianNoiseImageFilter . In practice, I personally do it in numpy with the python wrappings, see this article where I used this code: I0=1e7

Re: [Rtk-users] Few questions about FirstReconstruction.cxx

Hi, No, this is not a bug. This image is filled with 0 values so that's what you expect. This is the input image in which you are going to reconstruct. RayEllipsoidImageFitler calculates analytically the intersection between an ellipsoid defined by it's semi axes and it's density and the rays

Re: [Rtk-users] problem with installing RTK and Python

Yannick Grondin < yannick.gron...@surgiqual-institute.com> wrote: > Hi Simon, > > > > Thanks a lot, but it seems that you don’t have the wheel available for > Windows OS ? > > > > Thanks, > > > > Yannick > > > > *De :* Simon Rit [mailto:si

Re: [Rtk-users] Error in the FFTRampImpageFilter

here this 23 comes form ??? > > Anyway, it works fine now. Thank you. > Jérome > > > Le jeu. 7 mai 2020 à 20:48, Simon Rit a > écrit : > >> Hi, >> Nope, sorry. We can't distribute the package with FFTW because its >> license does not allow it. What you ca

Re: [Rtk-users] Insufficient Data For Proper Parker Weighting

h CUDA enabled. > > -- > *From:* Simon Rit > *Sent:* Tuesday, 30 June 2020 5:22 AM > *To:* Brani Rusanov > *Cc:* rtk-users@public.kitware.com > *Subject:* Re: [Rtk-users] Insufficient Data For Proper Parker Weighting > > Hi, > No, I

Re: [Rtk-users] Gantry rotation direction and artefacts

Mirror in which direction? Depending on the direction, it can also be a 180° offset of the angle. If it reconstructs well, I would assume that the direct direction is the correct one but there is something else you need to understand... On Fri, Aug 28, 2020 at 10:44 AM Vincent Libertiaux wrote:

Re: [Rtk-users] Gantry rotation direction and artefacts

ucted slice to get it in the right orientation, but I was wondering > where the issue comes from. > > Best regards, > Vincent > > On 28.08.20 12:13, Simon Rit wrote: > > Mirror in which direction? Depending on the direction, it can also be a > 180° offse

Re: [Rtk-users] Gantry rotation direction and artefacts

Hi Vincent, This sounds like a typical geometry problem. It's hard to guess what could be the problem without data. Is it a system for which you're able to reconstruct in the opposite direction? Simon On Thu, Aug 27, 2020 at 2:17 PM Vincent Libertiaux wrote: > Dear RTK users, > > I am trying to

Re: [Rtk-users] RTK library for Fan Beam CT Scan

Dear Ali, No need to send the same message more than once. It's possible to do fan-beam by managing the interpolations. For voxel-based backprojection, RTK does a bilinear interpolation on the detector so you need to add a line above and below each 1D projection. There is an example here

Re: [Rtk-users] How to fdk reconstruction properly

Hi, Input projections are selected with a path (-p) and a regular expression (-r) which are passed to an itk::RegularExpressionSeriesFileNames, see here . Your sinogram.mha file is 2D and RTK is meant for 3D. There

Re: [Rtk-users] Itk and rtk python install issues

erhaps it is a permissions > issue. The pre-compiled binaries are very convenient. To include CUDA > support, is building from source the only option? > > > > Andrew > > > > *From: *Simon Rit > *Date: *Tuesday, July 14, 2020 at 1:05 PM > *To: *Andrew Mark > *Cc

Re: [Rtk-users] Geometry Calibration and AddProjection Problem

Hi, I'm not sure why that is. Can you open an issue on github and I'll have a look when I get more time (not before the end of August)? I don't understand your second question, sorry. Can you detail what you want to do? Best regards, Simon On Fri, Jul 31, 2020 at 7:24 AM 童辰辰 wrote: > Hi Simon:

Re: [Rtk-users] R: Ring Artifacts correction

Hi Gabriele, There is nothing readily available in RTK, sorry. A PhD student working with me worked on that but using python scripts, see his PhD thesis here , chapter 7. Simon On Thu, Jul 9, 2020 at 2:57 PM wrote: > Dear all, > > I’m

Re: [Rtk-users] R: Ring Artifacts correction

Excellent! Thanks for sharing. On Thu, Jul 9, 2020 at 3:33 PM Samuel Gerber wrote: > This: https://github.com/InsightSoftwareConsortium/ITKRingArtifact > might be of interest. > > Best, > Sam > > > On Thu, Jul 9, 2020 at 9:30 AM Simon Rit > wrote: > >> Hi G

Re: [Rtk-users] Itk and rtk python install issues

e > build artifacts. > > > > Andrew > > > > *From: *Simon Rit > *Date: *Tuesday, July 14, 2020 at 12:16 PM > *To: *Andrew Mark > *Cc: *"rtk-users@public.kitware.com" > *Subject: *Re: [Rtk-users] Itk and rtk python install issues > > >

Re: [Rtk-users] Itk and rtk python install issues

Hi, I think the current RTK package on pypi is outdated wrt to ITK's. Either you use ITK v5.0.1 or you use the RTK package compiled by the CI. I think this one for example works. We will upload a new

Re: [Rtk-users] Insufficient Data For Proper Parker Weighting

send > them over. > > Kind regards, > Brani > -- > *From:* Simon Rit > *Sent:* Monday, June 15, 2020 8:59:19 PM > *To:* Brani Rusanov > *Cc:* rtk-users@public.kitware.com > *Subject:* Re: [Rtk-users] Insufficient Data For Proper Parker Weighting > > Hi,

Re: [Rtk-users] Reconstruction Artifact

that is allowed > > Thanks again! > Ben > > -- > *From:* Chao Wu > *Sent:* Wednesday, June 3, 2020 11:20 AM > *To:* Simon Rit > *Cc:* Andreas Andersen ; > rtk-users@public.kitware.com ; Benjamin W. > Maloney > *Subject:* Re: [Rtk-users] Reconstruction Artifa

Re: [Rtk-users] Reconstruction Artifact

ocessed in a float format. I wanted to check if there were >> restrictions on these float values. Can input image data have negative >> values or high values? Or are they expected to have values between 0 and 1? >> I ask because some of the tools I have used to do this prep

Re: [Rtk-users] Reconstruction Artifact

sample on a turntable with a fixed source and > detector but I believe that should be mathematically equivalent > > Thanks again! > Ben > -- > *From:* Simon Rit > *Sent:* Wednesday, June 3, 2020 1:04 PM > *To:* Benjamin W. Maloney > *Cc:* C

Re: [Rtk-users] Iterative Reconstruction inputs

Hi Ben, This should have been fixed since this commit . Maybe you can try to upgrade to RTK master? Otherwise, check the doxygen documentation or you can check here

Re: [Rtk-users] Blurry reconstructions in ROOSTER

Hi Erwin, I finally had time to look into this issue. I think the problem is that the conjugate gradient step is not the same in the two algorithms. If you carefully check Cyril's ROOSTER paper, he does not do a 3D conjugate gradient per phase but a 4D conjugate gradient. In your case, you have

Re: [Rtk-users] Reconstruction Artifact

Hi, Sometimes rotating in the wrong direction gives this kind of artefacts. It's quite possible that we don't use the same convention as other toolkits regarding this. For other questions: 1. Yes, you can use pixel as the unit. Then the image spacing should be 1 obviously and indeed, sdd and sid

Re: [Rtk-users] Water Precorrection - phantom

Hi, No really on my side. Most commercialized phantoms for QA have an homogeneous section which you can probably use to this end. Simon On Mon, Jul 27, 2020 at 4:03 PM wrote: > Dear RTK users and devs, > > I am planning to purchase or build a cylindrical shaped water phantom to > be exploited

Re: [Rtk-users] Building First Reconstruction

ts > > .txt > > FirstReconstruction.cxx > > LINK : fatal error LNK1104: cannot open file 'RTK.lib' [D:\Program > files\InsightToolkit-5.1.1\Modules\Remote\RTK\exampl > > es\FirstReconstruction\Build\FirstReconstruction.vcxproj] > > > > > > D

Re: [Rtk-users] ITK-RTK python install issues

Yes, sorry, we need to release binaries compatible with the latest ITK. Alternatively, you can downgrade the ITK packages to the v5.1.0 (maybe) or v5.0.1 (for sure) versions. Sorry for the trouble... Simon On Tue, Nov 24, 2020 at 4:22 PM Bleeker, M. (Margot) < m.blee...@amsterdamumc.nl> wrote: >

Re: [Rtk-users] Reconstruction from two eccentric short scans

Hi Gabriele, I ran your line codes. You're projections are not truncated so you can just work on one acquisition at a time. For the first simulation, I think that there is not enough data. That's unfortunate that RTK does not issue a warning, I have opened an issue

Re: [Rtk-users] Building First Reconstruction

Hi, Can you confirm that you have built ITK with Module_RTK ON also in Debug mode? See https://github.com/SimonRit/RTK/blob/master/INSTALLATION.md for some instructions. Simon On Fri, Nov 27, 2020 at 3:10 PM Bleeker, M. (Margot) < m.blee...@amsterdamumc.nl> wrote: > Hello, > > > > I am now

Re: [Rtk-users] Troubleshooting Conjugate Gradient Filter in Python

Hi, I slightly modified your script and it worked for me. What version are you using? I used the latest ITK v5.1.2 with, for RTK, an artifact published here (visible only if you're logged in github). Simon PS: I don't think you need the

Re: [Rtk-users] Troubleshooting Conjugate Gradient Filter in Python

ed numpy to 1.9.3 so itk could install > 5.1.2 and then installed the artifact you pointed for RTK. > Everything works fine now, time to play with the parameters! > > Clément > > > > Le ven. 18 déc. 2020 à 08:00, Simon Rit > a écrit : > >> Hi, >> I slightly mod

Re: [Rtk-users] SIRT Algorithm

Hi, I think SIRT comes down to using RTK SART and setting the number of projections per subset to the total number of projections. Simon On Sun, Dec 13, 2020 at 7:10 PM James Feng

Re: [Rtk-users] Help required - rtkFDK reconstruction

Hi, Please use the mailing list (cc). 1. The raw format is not directly understandable I believe, you need to have meta information passed, e.g. with a mhd. Since you know how to convert your projection images to line integral (for rtkfdk), just use the input of rtkfdk instead of using the

Re: [Rtk-users] FirstReconstruction questions

am given to reconstruct the > object > > Regards > lyh > > -- > *From:* Simon Rit > *Sent:* Wednesday, December 9, 2020 4:23 PM > *To:* Lai Yao Hao > *Cc:* rtk-users@public.kitware.com > *Subject:* Re: [Rtk-users] FirstReconstruction questions > > Hi, > constan

Re: [Rtk-users] FirstReconstruction questions

e when I used unsigned short on one computer but it works on > the other computer. > > Looking forward to your reply and answers! Much thanks in advance! > > Regards, > lyh > -- > *From:* Simon Rit > *Sent:* Wednesday, January 13, 2021 5:07 PM > *T

Re: [Rtk-users] FirstReconstruction questions

run these lines in the > terminal? > > Look forward for your favourable reply. > > With thanks > lyh > > > -- > *From:* Simon Rit > *Sent:* Tuesday, January 12, 2021 4:22 AM > *To:* Lai Yao Hao > *Cc:* rtk-users@public.kitware.com &g

Re: [Rtk-users] FirstReconstruction questions

ighlighted inputs? > > Appreciate your advice and look forward for your reply! > > Regards > lyh > -- > *From:* Simon Rit > *Sent:* Wednesday, January 27, 2021 6:21 PM > *To:* Lai Yao Hao > *Cc:* rtk-users@public.kitware.com > *S

Re: [Rtk-users] Elekta / kV-kV image Reconstruction and Test dataset

Hi, 1. Yes, simply change the dimension and origin to make it 3D, for example to --dimension 1024 --origin -127.875 which will set the same values for the three dimensions. 2. No, you need more than 2 projection to reconstruct a 3D image. I think you need to read some books on tomography to

Re: [Rtk-users] Elekta / kV-kV image Reconstruction and Test dataset

ake reconstruction? > > I know some proton/photon Radiotherapy device can reconstruct these > images, like Varian TrueBeam/Probeam, IBA Proteus. > > > BR, > George > > ‐‐‐ Original Message ‐‐‐ > On 2021年5月21日FridayPM3点21分, Simon Rit > wrote: > > Hi,

Re: [Rtk-users] FW: Elekta CBCT Reconstrution

+, an AT 5G Evolution capable smartphone > Get Outlook for Android <https://aka.ms/AAb9ysg> > ---------- > *From:* Hamed Hooshangnejad > *Sent:* Friday, July 2, 2021 8:57:01 AM > *To:* Simon Rit > *Cc:* rtk-us...@openrtk.org > *Subject:* RE: FW: Elekta CBCT Reconstrution &

[Rtk-users] Release of RTK v2.2.0

gnment with ITK developments * Enhanced Python wrappings * Many compilation, bug and style fixes Many thanks to all contributors for this release, in alphabetical order: Sebastien Brousmiche, Aurélien Coussat, Julien Finet, Lucas Gandel, Hans Johnson, Matt McCormick, Antoine Robert, MrTzschr, Simon Rit,

Re: [Rtk-users] FirstReconstruction questions

orrect, is > it possible to suggest steps which I can read the projections correctly > with the correct spacing and origin? > > Thanks in advance for the advice and I look forward towards your reply! > > Regards > lyh > -- > *From:* Simon Rit > *Sen

Re: [Rtk-users] Error message at commit time

Hi, I just compared RTK's .gitattribute file and ITK's. Can you try removing ",uncrustify" from RTK .gitattribute file to see if that fixes the issue? Thanks, Simon On Fri, Mar 26, 2021 at 6:37 PM Jerome Lesaint wrote: > Hi all, > > Here the situation : i've made somme changes on a local copy

Re: [Rtk-users] Ring artifact even with homogenous valued projection

gt;SetZeroPadFactors(2); > but neither seemed to make a difference. > > I didn't see any other pad functions though > > Thanks! > Ben > -- > *From:* Simon Rit > *Sent:* Friday, April 2, 2021 4:51 PM > *To:* Benjamin W. Maloney > *Cc:*

Re: [Rtk-users] Ring artifact even with homogenous valued projection

Hi, If you pass homogeneous non-zero images, you expect such a ring artefact. The reason is that FDK assumes non-truncated projections, i.e., the projections should be 0 at the border. If not, then the ramp filtering will make a transition from the value to 0. Probably, your projections are

Re: [Rtk-users] Creating DRRs with RTK in python

Hi, Both your input volume and your stack of projections should be 3D. If you simulate only one projection, you can always make it 2D afterwards by slicing the stack. The third dimension of spacing and origin of the stack are never used in RTK but must be provided since it's a 3D image. I might be

Re: [Rtk-users] JosephForwardProjectionImageFilter - output intensity problem

Hi, I'm not sure but one thing is that after reconstruction, you should mask out everything which is out of the field of view. This can be done with the FieldOfViewImageFilter to which you should pass the reconstructed image

Re: [Rtk-users] reconstruction of pinhole collimator

Hi, I don't think anyone has done such a reconstruction so far. For parallel SPECT, there is an example in the osem test with attenuation correction : https://github.com/SimonRit/RTK/blob/master/test/rtkosemtest.cxx#L226L230 but I'm not sure they are directly applicable to divergent geometries.

Re: [Rtk-users] Creating DRRs with RTK in python

ible to change around > which axis the projections are made? And is it also possible to first do a > rotation around the z axis and then the y axis leading to 360x360 > projection images? > > > > Thank you very much. > > > > Best regards, > > Milou > >

Re: [Rtk-users] Question about RTK SART reconstruction

Hi, Thanks for your interest. Prefer the mailing list (cc) for your questions. rtkSARTConeBeamReconstructionFilter can use the GPU by setting GPU forward and backprojectors, simply set the adequate projector. For example, check rtksart

Re: [Rtk-users] Python RTK + CUDA

Hi Gabriele, You can check the example here . Note, however, that the CUDA python packages are still not distributed. The ones on pypi only have CPU code. So you would need to compile the python

[Rtk-users] Release of RTK v2.3.0

on, CI and install. Many thanks to all contributors for this release, in alphabetical order: Lucas Gandel, Laurent Malka, Antoine Robert, Simon Rit and Tomoyuki Sadakane. As usual, be aware that we do not focus on releases since we have a public github repository that we aim at keeping stable. I

Re: [Rtk-users] the source code of non cuda version

Hi, Please use the RTK mailing list (cc). The CPU code is templated to be able to use different types (double, float, etc.). The source code is here , in an hxx file the include subfolder. You can check the

Re: [Rtk-users] CudaImage not found in Python RTK

Hi, The pypi package does not have the Cuda option. Using cuda in wrapping requires to compile it yourself, see INSTALLATION.md . Providing pypi packages cuda is a difficult task which we are still working on... Simon On Fri, Dec 17,

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