Re: [Rtk-users] How to use RTK to reconstruction 2D X- ray Scan projection images into 2D CT Slice image?

--- > > 2. You can reconstruct one 3D slice by using a size of 1 in the axial > direction > --> Do you mean Set Z in the size parameter to 1 ? > for example --> Size (XYZ)=>(1024,1024,1) > then I get the reconstruct image like this ? > > [image:

Re: [Rtk-users] How to use RTK to reconstruction 2D X- ray Scan projection images into 2D CT Slice image?

Hello, 1/ Yes, you can read images in raw format but you need to specify the meta information for example in python rawio = itk.RawImageIO.New() rawio.SetNumberOfDimensions(2) rawio.SetPixelType(itk.CommonEnums.IOPixel_SCALAR) rawio.SetComponentType(itk.CommonEnums.IOComponent_FLOAT)

Re: [Rtk-users] there is a higher density area at the center of hole

Hi, It's a bit hard to guess... I guess an issue with the geometry might cause such an artefact, e.g. a wrong detector offset in the direction perpendicular to the axis of rotation. Simon On Fri, Dec 16, 2022 at 2:45 AM 王冬平 wrote: > hi Simon > i reconed one phantom with holes, but i found there

Re: [Rtk-users] ITK ERROR: Geometry is empty error when generating DRRs

t; > Could you please assist me in resolving these two problems ? Thanks in > advance for your time and consideration. > > > > On Mon, Dec 12, 2022 at 3:08 PM Simon Rit > wrote: > >> Hi, >> 1) You can't. This method uses another parametrization. >> 2)

Re: [Rtk-users] ITK ERROR: Geometry is empty error when generating DRRs

m to produce DRRs with aforementioned machine > configurations in AddProjection method ? > > > > On Mon, Dec 12, 2022 at 8:43 AM Simon Rit > wrote: > >> Hi, >> You might have missed an earlier message >> WARNING: In >> /home/srit/src/itk/itk/Modules/Remote/

Re: [Rtk-users] ITK ERROR: Geometry is empty error when generating DRRs

Hi, You might have missed an earlier message WARNING: In /home/srit/src/itk/itk/Modules/Remote/RTK/src/rtkThreeDCircularProjectionGeometry.cxx, line 210 DataObject (0x55d436d7ee10): Failed to AddProjection The problem is that the two vectors describing the projection orientation are not unit

Re: [Rtk-users] DRR with limited FOV from 3D-CT

are attached. > > I highly appricate your willingness to help me on this please. > > > On Sat, Nov 12, 2022 at 6:06 AM Simon Rit > wrote: > >> Hi, >> The anatomical orientation is not used by RTK. >> Simon >> >> On Fri, Nov 11, 2022 at 11:43 AM Isuru

Re: [Rtk-users] Ray-tracing through a binary mask image volume

Dear Suranga W, I'm not sure what you expect but I think that the problem is that you're adding 1000 to your mask in the code. If you removing this "CTarray += 1000" line, I see better the liver mask in the projection. Simon On Mon, Nov 28, 2022 at 12:13 PM Suranga W <

Re: [Rtk-users] Does RTK support a scanner with fixed source and detector?

Hi, The geometric parameters of AddProjection, used in rtksimulatedgeometry.cxx , are described in the documentation here . The artifact

[Rtk-users] Release of RTK v2.4.1

Dear RTK users, RTK v2.4.1 has just been released. This release is intended to produce Python packages compatible with the ITK Python packages v5.3rc04.post4. I have also moved the repository to the RTKConsortium organization so please

Re: [Rtk-users] DRR with limited FOV from 3D-CT

hat could be the cause ? > RAS_oriented_ref_CT.nii.gz > <https://drive.google.com/file/d/1ypdqeQQpbvjy7k4T_zxY3e8g3-fhmI5q/view?usp=drive_web> > > > > On Thu, Nov 10, 2022 at 7:22 AM Simon Rit > wrote: > >> Hi, >> ref_CT_updated.nii.gz is still not oriented co

Re: [Rtk-users] DRR with limited FOV from 3D-CT

google.com/file/d/1BntJvZ7JRF9kTxQsycB5JoipWVFESNQ_/view?usp=drive_web> > rtk_drr_projection_code.txt > <https://drive.google.com/file/d/1mEaIbj9NjuU5BZB4NKlmv0S9CUN0FME3/view?usp=drive_web> > > > > > On Wed, Nov 9, 2022 at 2:26 PM Simon Rit > wrote: > >&

Re: [Rtk-users] DRR with limited FOV from 3D-CT

Hi, The first input of JosephForwardProjectionImageFilter is the image in which you'll calculate the DRR, typically an empty projection (filled with zeros). In your code, this is computed with constantImageSource but you're setting the volume origin, spacing size which is probably wrong. For an

Re: [Rtk-users] Release of RTK v2.4.0

Please note that we have released CUDA-compatible version <https://pypi.org/project/itk-rtk-cuda116> of RTK Python packages with this release, see itk-rtk-cuda116 in INSTALLATION.md <https://github.com/SimonRit/RTK/blob/master/INSTALLATION.md>. On Sat, Oct 29, 2022 at 9:09 AM Simo

[Rtk-users] Release of RTK v2.4.0

ikhail Polkovnikov, MrTzschr, Shengpeng YU, Simon Rit and Tom Birdsong. The next release will be a major one which will split the ITKCudaCommon code in a separate ITK module. Simon (for the RTK consortium) ___ Rtk-users mailing list Rtk-users@public.kitwa

Re: [Rtk-users] (no subject)

Hi, The preprocessing is described with a graph at http://www.openrtk.org/Doxygen/classrtk_1_1ProjectionsReader.html Follow the Elekta path. I0 is used by LUTbasedVariableI0RawToAttenuationImageFilter .

Re: [Rtk-users] DRR from 3d CT and projection of lung contour mesh onto it

Hi qod rec, 1. The projection is limited by the size of your input volumes. With such a large source to object distance (10 m), you're almost parallel so what you see should correspond to the size of a coronal slice of your volume. 2. constantImageSource creates an image (here filled with the

Re: [Rtk-users] Reconstructing DICOM data

; <https://drive.google.com/file/d/11COT9G6jzrHALPvUs8N4jnnZt9kuIMd3/view?usp=drive_web> > > Regards, > Sreejith > > On Tue, Sep 20, 2022 at 12:44 PM Simon Rit > wrote: > >> Hi, >> Your projections in Ankle.mha display a very large value in air. T

Re: [Rtk-users] Issues with displaced detector filter when running FDK inline with acquisition

s without any issues. > > > > Kind regards, > > Nick > > > > *Van:* Simon Rit > *Verzonden:* Tuesday, September 20, 2022 9:25 AM > *Aan:* Nick Staut > *CC:* rtk-users@public.kitware.com > *Onderwerp:* Re: [Rtk-users] Issues with displaced detector filter wh

Re: [Rtk-users] Issues with displaced detector filter when running FDK inline with acquisition

Hi Nick, I stopped caring about the inline application and removed it as it did not seem to be used... One of the things that has been developed is a new weighting scheme for offset detectors, see doi.org/10.1118/1.4945418. In this filter, you cannot specify the minimum and maximum offsets

Re: [Rtk-users] Reconstructing DICOM data

Hi, Your projections in Ankle.mha display a very large value in air. To start with, I would make sure that everything outside the leg is at about 0 in your original Ankle CT data. Note that projecting and reconstructing a CT image will necessarily result in a loss of quality due to the multiple

Re: [Rtk-users] Acceleration of rtkCudaBackProjectionImageFilter

Dear Laura, Interesting, this option is mainly here for improving the memory management. All it does is split your input stack in subsets to do the reconstruction, thus only loading a few projections in the CPU and GPU memory. This is not implemented in the backprojection because we usually keep

Re: [Rtk-users] Rtk reconstruction

t it to geometry file in order to reconstruct. Will > these script are enough? If yes, where I can input my raw file? > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows > > > > *From: *Simon Rit > *Sent: *Wednesday

Re: [Rtk-users] (no subject)

Hi, You need to download the file https://data.kitware.com/api/v1/item/5b179c938d777f15ebe2020b/download. Simon On Wed, Aug 17, 2022 at 8:24 AM Rakib Hossain wrote: > I have followed Script/FDK. In 2nd step *# Create projections of the phantom > file* > > rtkprojectgeometricphantom -g

Re: [Rtk-users] CBCT reconstruction from CT DICOM

Hi, Please check the geometry documentation http://www.openrtk.org/Doxygen/DocGeo3D.html For example, rtksimulatedgeometry uses it, in C++ or in Python

Re: [Rtk-users] Back Projection

ype1::New(); > > reader1->SetFileNames(fileNames); > > reader1->Update(); > > using BackFilter = rtk::CudaFDKConeBeamReconstructionFilter; > > auto BackProjFilter = BackFilter::New(); > > // FDK reconstruction > > std::cout << "Reconstruc

Re: [Rtk-users] scatter correction

g and straight forward. > > Could you share some result? > > > > Regards > > > > Wang Dongping > > > > *发件人:* Simon Rit > *发送时间:* 2022年7月10日 22:00 > *收件人:* dongping.w...@simmhealthcare.com > *抄送:* rtk-users > *主题:* Re: [Rtk-users] scatter correct

Re: [Rtk-users] Back Projection

Hi, It should work. UpdateOutputInformation is not required (it's done by Update already). Does the outputImage passed as input to the backprojection have the same information as reader->GetOutput()? Simon On Fri, Aug 12, 2022 at 8:57 AM Adarsh S Sunil wrote: > > Hi all, > > I'm a

Re: [Rtk-users] Lateral blur in a FDK reconstructed volume

, I'm not sure you can trust this information... as I don't know where it comes from. Best regards, Simon On Tue, Jul 19, 2022 at 11:34 AM Vincent Libertiaux wrote: > On 11.05.22 15:20, Vincent Libertiaux wrote: > > On 11.05.22 15:15, Simon Rit wrote: > > Hi, > Yes, I think it's c

Re: [Rtk-users] reading Elekta database projections

mon, > Thanks, this works. Could you please also describe how to read geometry > from the xml file into a geometry variable? > Thanks a lot. > > > Best, > Rupesh > > > On Mon, Jul 18, 2022 at 2:08 AM Simon Rit > wrote: > >> Hi, >> To

Re: [Rtk-users] reading Elekta database projections

Hi, To read in the projections, you should create an array with the filenames (name filenames below) and then ImageType = itk.Image[itk.F, 3] proj = rtk.ProjectionsReader[ImageType].New() proj.SetFileNames(filenames) proj.Update() nparray = itk.GetArrayFromImage(proj.GetOutput()) This should work.

Re: [Rtk-users] scatter correction

Hi Wang Donging, Only an implementation of Boellaard's scatter correction is available and I'm not convinced that the implementation is correct (see here ). We have used other corrections which are not available in RTK such as Monte Carlo scatter

Re: [Rtk-users] projection normalization

xpert. > > Regards, > Howard > > On Tue, Jun 28, 2022 at 5:41 PM Simon Rit > wrote: > >> Hi, >> 1) I think I would divide the measured projection by the flood field, no >> reason to limit it to one scalar. The rest seems correct. >> > > Yes, what I did befo

Re: [Rtk-users] projection normalization

Hi, 1) I think I would divide the measured projection by the flood field, no reason to limit it to one scalar. The rest seems correct. 2) yes! But with a spectrum, it's hard to anticipate the ref value due to beam hardening. 3) It's "normal" to have negative values due to scatter, not beam

Re: [Rtk-users] projection geometry offset

Hi, I guess the confusion comes from "“The detector position is defined with respect to the source with three parameters”. I guess we wrote this due to the use of source distances in the third coordinate SourceToIsocenterDistance-SourceToDetectorDistance, but it's with respect to the isocenter

Re: [Rtk-users] orientation messed up in cbct recon

Hi, I think you should refer to the geometry documentation: http://www.openrtk.org/Doxygen/DocGeo3D.html In RTK, the rotation axis is y (whereas it's z in Dicom). So there is probably nothing wrong... Simon On Wed, May 11, 2022 at 4:03 PM Howard wrote: > Hi, > > I had some geometric questions

Re: [Rtk-users] Lateral blur in a FDK reconstructed volume

#a0fb1475ed76a28cde24fac85eae18e1e and then check the resulting angles and distances. Simon On Wed, May 11, 2022 at 2:15 PM Vincent Libertiaux wrote: > On 10.05.22 22:54, Simon Rit wrote: > > Hi Vincent, > > RTK can parametrize any orientation of the detector with the three > > angles Gant

Re: [Rtk-users] Lateral blur in a FDK reconstructed volume

, detector position, u axis and v axis in patient/object coordinates to derive the RTK parameters. Good luck with this! Simon On Tue, May 10, 2022 at 5:23 PM Vincent Libertiaux wrote: > On 25.04.22 09:07, Simon Rit wrote: > > Hi Vincent (and Jasper), > I agree with Jasper that this is mos

Re: [Rtk-users] rtk::ThreeDCircularProjectionGeometry:: VerifyAngles() epsilon question

Hi Brandon, Thanks for the detailed report and sorry for the late answer. To be honest, I'm not sure what is the appropriate fix here and I still haven't found the time to look into it. Could you please open an issue on github to keep track of this? You can just copy paste your email in it.

Re: [Rtk-users] Lateral blur in a FDK reconstructed volume

Hi Vincent (and Jasper), I agree with Jasper that this is most likely due to a difference in geometric calibration between the two datasets. Do you have more information on what does B use (projection matrices, detailed parametrization, etc.)? I think that such a blur can be caused by a difference

[Rtk-users] PhD fellowship: Exponential DCC for patient motion detection and correction in SPECT

The CREATIS laboratory (Lyon, France) opens a PhD fellowship on the topic of exponential data consistency conditions (DCC) for patient motion detection and correction in single-photon emission computed tomography (SPECT): https://www.creatis.insa-lyon.fr/site7/en/node/47190 Location: CREATIS,

Re: [Rtk-users] Using itkMaximumProjectionImageFilter with RTK?

Hi, I haven't done it but you should be able to do it with JosephForwardProjectionImageFilter by setting your own TProjectedValueAccumulation instead of the default one

Re: [Rtk-users] Forward projection rotation matrix from gantry and couch angles

Hi, I would rather suggest another version of AddProjection which uses the source position, detector origin position, u and v vectors. Be aware that FBP assumes that the rotation is

Re: [Rtk-users] rtksart exception error

Np pb and thanks for the feedback! Simon On Thu, Feb 24, 2022 at 11:48 AM Vincent Libertiaux wrote: > On 24.02.22 10:02, Simon Rit wrote: > > Hi, > It seems that CMake has trouble finding Cuda. What version of cmake are > you using? Is your cmake variable CMAKE_CUDA_COMPILER set

Re: [Rtk-users] rtksart exception error

Hi, It seems that CMake has trouble finding Cuda. What version of cmake are you using? Is your cmake variable CMAKE_CUDA_COMPILER set to the correct nvcc compiler? A similar problem has been reported for the CudaCommon package so I'm not sure I

Re: [Rtk-users] rtksart exception error

ks for you too before I merge. Simon On Wed, Feb 23, 2022 at 3:19 PM Vincent Libertiaux wrote: > On 23.02.22 11:32, Simon Rit wrote: > > Hi Vincent, > Thanks. I cannot reproduce the issue on my laptop is I only modify the > size of the reconstructed volume with

Re: [Rtk-users] rtksart exception error

Hi Vincent, Thanks. I cannot reproduce the issue on my laptop is I only modify the size of the reconstructed volume with "--dimension 2500,2500,10". With this argument, do you still have the same issue? I am suspecting that a problem occured before (e.g., memory allocation failing) and I would

Re: [Rtk-users] rtksart exception error

Hi Vincent, I'm not sure. The copy to a pitched array is failing but I'm not sure why. Can you share the geometry file and the header of the projections to check what could be the problem? Simon On Tue, Feb 22, 2022 at 3:03 PM Vincent Libertiaux wrote: > Hello RTK users, > > I am trying to

Re: [Rtk-users] 3D Backprojection using 360 X-ray 2D images

Hi Fernando, I'm continuing the github conversation in PR #472 on the mailing list, it feels more adequate. There is obviously a geometry problem but despite spending a bit of time on it, I could not find the solution. In the data you sent, there is an

Re: [Rtk-users] 3D Backprojection using 360 X-ray 2D images

Hi, FDK takes as second input a stack of projections images, not a constant image. You need to convert your projections to line integrals. Instead of using an ImageFileReader, you can use rtk::ProjectionsReader does this for you.

Re: [Rtk-users] RTK has no ElektaXVI5GeometryXMLFileReader at python

Hi, It's been added but not released on pip yet. You can use a package compiled on github actions which can be downloaded if you're logged in github, e.g., here: https://github.com/SimonRit/RTK/actions/runs/1788462136 in the artifacts section. You are welcome to write other python applications and

Re: [Rtk-users] rtk.cxx imports real projection data

Hi, The idea of the the applications like rtkfdk.cxx is to use gengetopt, a command line parser, to pass options. See for example https://wiki.openrtk.org/index.php/RTK/Scripts/FDK What is actually done for the projections reader is here

Re: [Rtk-users] About flat field correction for elekta CBCT data

Hi, Yes, flat field correction is possible with ITK since it's the log of the division of two images. We do it for example for some data types (for example the XRad small animal scanner, see here

Re: [Rtk-users] How do I compile the files in the wrapping folder?

Hi, To compile python packages, you must turn on ITK_WRAP_PYTHON. For example, I use cmake $SCRIPT_PATH/itk \ -DITKPythonPackage_ITK_BINARY_REUSE:BOOL=OFF \ -DITKPythonPackage_WHEEL_NAME:STRING="itk" \ -DCMAKE_BUILD_TYPE=RelWithDebInfo \ -DBUILD_EXAMPLES=OFF \

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,

Re: [Rtk-users] About the Elekta Reconstruction DBF file

rsion table of the elekta system? > I checked rtkElektaSynergyRawLookupTableImageFilter.h and > ElektaSynergyLookupTableImageFilter.h , > but I couldn't understand the difference between each source code because > I didn't study C ++ yet. > > Best regards. > > masa > > 2021年12月1日(水) 0:21 Simon R

Re: [Rtk-users] About the Elekta Reconstruction DBF file

Hi, Yes, this mailing list is meant for this kind of questions. Only this information is used, see here . To understand the meaning, you can check that it's used here

Re: [Rtk-users] Unable to compile FirstReconstruction example with CUDA support

Hi, Thanks for the report. I can reproduce the error and I have tried to fix it without any success so far, at least for all configurations (RTK compiled within or outside ITK, use install or build, etc.). We are in the process of moving ITKCudaCommon to a separate repository, rather than spending

Re: [Rtk-users] CBCT reconstruction

Hi, It's hard to help without having a look at your dcm files. From the screenshot, it seems that your projections are very small, I would check the pixel size of them and whether they are centered. Simon On Fri, Nov 26, 2021 at 9:44 AM Attila Nagy wrote: > Hi, > > I have 20 projections of a

Re: [Rtk-users] Could not create IO object when using rtkForwardProjections application with NRRD file

Hi, Indeed. I think it depends on the options set here . You can add NRRD on your local compilation but I don't think it is of general interest to add all IO factories. If you build your own application, you can add it to your

Re: [Rtk-users] Slow CUDA FDK performance

ctionFilter.hxx#L49-L56> > . > > So a simple > > CPUSuperclass::SetProjectionSubsetSize(SLAB_SIZE); > > In the constructor of CudaFDKConeBeamReconstructionFilter should be enough? > Or am I approaching the issue from the wrong side and mixing up things? > > > > Best

Re: [Rtk-users] Slow CUDA FDK performance

; # define SLAB_SIZE 16 > > #endif > > > > Do you have an explanation why this gets reduced from 16 to 2? Or a hint > where I can have a look? > > > > Best, > > Moritz > > > > > > *Von:* Simon Rit > *Gesendet:* Donnerstag, 18. November 2021

Re: [Rtk-users] Slow CUDA FDK performance

> > Looks like there was a typo in my mail, the versions compared should be: > > old: CUDA 10.2, ITK 5.1.2, RTK 2.1.0 > > new: CUDA 11.5, ITK 5.2.1, RTK 2.3.0 > > > > Sorry for the confusion and thanks for looking into it! > > > > Best, > > Moritz &

Re: [Rtk-users] Slow CUDA FDK performance

Hi Moritz, Thanks for the report. It's a bit hard to be convinced that something is wrong without being able to reproduce it. From the RTK_PROBE_EACH_FILTER log, most of the time is spent reading the projections which will be the same with or without cuda so I wonder if this is not the issue here.

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

[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] 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

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] 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] 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

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] 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 &

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] 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] 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] 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] 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] 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

[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

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

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] 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] 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] 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] R: Trying to reconstruct with a 180 degrees circular projection geometry

am using to acquire data can > only rotate 180° around the patient but is still able to reconstruct (I > don't have access to the projections, it generates a 3d volume as output). > Are you aware of any algorithm that would be able to do so? > > Clément > > Le ven. 11 déc. 2020 à

Re: [Rtk-users] R: Trying to reconstruct with a 180 degrees circular projection geometry

Hi Clément, To complement Gabriele's response and explains what goes on. FDK requires a 360° acquisition. RTK will calculate the angular gap between the current projection and the two neighbors. With your configuration, two projections take an angular weight (the delta when discretising the

Re: [Rtk-users] ThreeDCircularProjectionGeometry Angular Arc

Hi, You're right, it's better to cover slightly more than 360 degrees if the scanner follows the same piece of trajectory at the beginning and at the end (on a circle since you're using FDK). Rotation angles are currently forced between 0 and 2 pi, see here

Re: [Rtk-users] FirstReconstruction questions

Hi, constantImageSource creates a constant volume. In the example, one is used as input of the simulation of projections of an ellipsoid (rei) and one as input of the reconstruction algorithm (feldkamp). fieldofview masks out (i.e., set to 0) voxels which are not in the field of view. I don't

Re: [Rtk-users] detector with not multiple pixel gap

Hi Julia, The artifact on the first image is not obvious to me. Can you clarify which artifact is visible on the first image but not on the second? In the second image, is the gap exactly at the center of the image? If yes, I don't see a better solution than interpolating between adjacent pixels.

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

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] 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] 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] How to fill an outer space with air in forward projection

Hi, RTK forward projector only does the line integral of the volume. You should try to find what Plastimatch does exactly but I would try to add the following operations: - Make air at 0 (if HU, air is at -1000 so add 1000 to your input volume) - forward project - multiply by -1 and take the log

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] 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] 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

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