# Latest

**URL:** https://discourse.itk.org/latest.md?page=52

[Latest](https://discourse.itk.org/latest.md) · [Categories](https://discourse.itk.org/categories.md) · [Tags](https://discourse.itk.org/tags.md)

**Page:** 53

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## [No module named '\_SimpleITK' after installing SimpleElastix #424](https://discourse.itk.org/t/no-module-named-simpleitk-after-installing-simpleelastix-424/4022)

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**Author:** [@Fleur](https://discourse.itk.org/u/Fleur)\
**Replies:** 3\
**Last updated:** [April 13, 2021, 12:26pm UTC](https://discourse.itk.org/t/no-module-named-simpleitk-after-installing-simpleelastix-424/4022 "2021-04-13T12:26:10Z")

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Dear all, I apologize in advance if this forum is the wrong place to raise this issue, which is more related to SimpleElastix than simpleITK. I did not get any answer from the SimpleElastix community, so I’m trying here…

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## [large size when saving image using SimpleITK WriteImage](https://discourse.itk.org/t/large-size-when-saving-image-using-simpleitk-writeimage/3509)

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**Author:** [@ibr](https://discourse.itk.org/u/ibr)\
**Replies:** 2\
**Last updated:** [April 12, 2021, 3:30pm UTC](https://discourse.itk.org/t/large-size-when-saving-image-using-simpleitk-writeimage/3509 "2021-04-12T15:30:28Z")

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Dear all, when I save image using SimpleITK the file size are larger than the one are saved using in 3D Slicer e.g. imoprt SimpleITK as sitk img = sitk.ReadImage("imageFilename.nii.gz") img = sitk.Cast(img, sitk.sitkIn…

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## [How to get a smoother region combining all the islands of my segmentationmask?](https://discourse.itk.org/t/how-to-get-a-smoother-region-combining-all-the-islands-of-my-segmentationmask/4026)

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**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 2\
**Last updated:** [April 12, 2021, 4:09am UTC](https://discourse.itk.org/t/how-to-get-a-smoother-region-combining-all-the-islands-of-my-segmentationmask/4026 "2021-04-12T04:09:08Z")

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As shown here, I have multiple components of small regions. I don’t want to remove any islands. But I want to combine all of them into a single region. I have been using SimpleITK for a while and tried various hole fi…

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## [3D point coordinates projection issue on the DRR image plane](https://discourse.itk.org/t/3d-point-coordinates-projection-issue-on-the-drr-image-plane/4018)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 5\
**Last updated:** [April 8, 2021, 2:33pm UTC](https://discourse.itk.org/t/3d-point-coordinates-projection-issue-on-the-drr-image-plane/4018 "2021-04-08T14:33:08Z")

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I have implemented a code to get the corresponding 2D projection coordinate (i.e. x, y positions) of each vertex coordinate (i.e. 3D) on the DRR image projection plane. But, I have a problem regarding this DRR projectio…

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## [Job opportunities at Kitware](https://discourse.itk.org/t/job-opportunities-at-kitware/3993)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 1\
**Last updated:** [April 8, 2021, 12:39am UTC](https://discourse.itk.org/t/job-opportunities-at-kitware/3993 "2021-04-08T00:39:13Z")

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There are several job opportunities for talented software developers and research and development engineers in the Medical Group at Kitware. We are open to candidates who can work from one of our branch offices or remote…

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## [How to get the desired voxel index for region growing algorithms by using VTK voxel index?](https://discourse.itk.org/t/how-to-get-the-desired-voxel-index-for-region-growing-algorithms-by-using-vtk-voxel-index/4016)

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**Author:** [@happyITK](https://discourse.itk.org/u/happyITK)\
**Replies:** 6\
**Last updated:** [April 7, 2021, 2:18pm UTC](https://discourse.itk.org/t/how-to-get-the-desired-voxel-index-for-region-growing-algorithms-by-using-vtk-voxel-index/4016 "2021-04-07T14:18:44Z")

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Hi everyone! I’m a beginner of ITK and VTK.Now I want to use the 3D region growing algorithms to segment specific tissues.But I’m confused how to get the voxel index. I have finished the vulume rendering and could get …

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## [KeyError: 'ITKSmoothing' when initializing RegularStepGradientDescentOptimizerv4](https://discourse.itk.org/t/keyerror-itksmoothing-when-initializing-regularstepgradientdescentoptimizerv4/3973)

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**Author:** [@Soren\_Christensen](https://discourse.itk.org/u/Soren_Christensen)\
**Replies:** 5\
**Last updated:** [April 7, 2021, 1:54am UTC](https://discourse.itk.org/t/keyerror-itksmoothing-when-initializing-regularstepgradientdescentoptimizerv4/3973 "2021-04-07T01:54:56Z")

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Hi, I have a fresh pip install of 5.1.1 and get this error when creating an ImageRegistrationMethodv4 object: registration = itk.ImageRegistrationMethodv4.REGv4F3F3.New(FixedImage=fixed, …

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## [MultiLabelSTAPLEImageFilter does not work](https://discourse.itk.org/t/multilabelstapleimagefilter-does-not-work/4003)

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**Author:** [@Fleur](https://discourse.itk.org/u/Fleur)\
**Replies:** 2\
**Last updated:** [April 6, 2021, 5:03pm UTC](https://discourse.itk.org/t/multilabelstapleimagefilter-does-not-work/4003 "2021-04-06T17:03:56Z")

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Dear all, I’m trying to use MultiLabelSTAPLEImageFilter to combine several segmentations. However, when I run the code, nothing happens. The code seems to be running for hours, and calling ctrl + C to stop it does not …

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## [How to install an earlier release of ITK](https://discourse.itk.org/t/how-to-install-an-earlier-release-of-itk/4013)

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**Author:** [@arswitze](https://discourse.itk.org/u/arswitze)\
**Replies:** 3\
**Last updated:** [April 6, 2021, 12:49pm UTC](https://discourse.itk.org/t/how-to-install-an-earlier-release-of-itk/4013 "2021-04-06T12:49:59Z")

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Hello, I am trying to use a tool called PETPVC which requires the insight toolkit. I built and installed ITK version 5.1 on MacOSX15, however, I am unable to build PETPVC in Cmake because of a missing CylinderSpatialObj…

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## [How to generate the attenuation matrix?](https://discourse.itk.org/t/how-to-generate-the-attenuation-matrix/4005)

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**Author:** [@Massoud](https://discourse.itk.org/u/Massoud)\
**Replies:** 3\
**Last updated:** [April 5, 2021, 9:22pm UTC](https://discourse.itk.org/t/how-to-generate-the-attenuation-matrix/4005 "2021-04-05T21:22:19Z")

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Hi everyone, I am using rtkfdk.exe to generate 3D image by using measured input projections (0-360 degree) and the Geometry.xml file. I would like to extract the attenuation matrix (Ax=p) where x is the 3D image matrix …

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## [Issue with SetSpacing](https://discourse.itk.org/t/issue-with-setspacing/4011)

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**Author:** [@archsci](https://discourse.itk.org/u/archsci)\
**Replies:** 1\
**Last updated:** [April 5, 2021, 8:00pm UTC](https://discourse.itk.org/t/issue-with-setspacing/4011 "2021-04-05T20:00:27Z")

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Hello, I am trying to create an itk image from numpy array. I have, itkImg = itk.GetImageFromArray(array) itkImg.SetOrigin(\[1.0, 1.0, 1.0\]) itkImg.SetSpacing(\[1.0, 2.0, 2.0\]) After creating the image, I want to change…

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## [SimpleITK Apply VersorRigid3DTransform to Image Direction](https://discourse.itk.org/t/simpleitk-apply-versorrigid3dtransform-to-image-direction/3995)

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**Author:** [@Nick\_Rubert](https://discourse.itk.org/u/Nick_Rubert)\
**Replies:** 1\
**Last updated:** [April 1, 2021, 7:39pm UTC](https://discourse.itk.org/t/simpleitk-apply-versorrigid3dtransform-to-image-direction/3995 "2021-04-01T19:39:54Z")

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Hi board, Is there an easy way to apply a VersorRigid3DTransform to a SimpleITK image direction and get the corresponding transformed image direction? Another way to state my question might be: Are there easy ways to g…

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## [FFTW, MKL, CUFFT and USE\_GPU](https://discourse.itk.org/t/fftw-mkl-cufft-and-use-gpu/3348)

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**Author:** [@gdevenyi](https://discourse.itk.org/u/gdevenyi)\
**Replies:** 10\
**Last updated:** [April 1, 2021, 6:43pm UTC](https://discourse.itk.org/t/fftw-mkl-cufft-and-use-gpu/3348 "2021-04-01T18:43:39Z")

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I notice there’s quite a few “accelerator” type options for ITK builds, but the documentation regarding what they do/impact is very sparse to non-existent. Can anyone point me at some docs, or enlighten me as to how muc…

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## [Split/Crop 3d Image slices into 3d small objects.](https://discourse.itk.org/t/split-crop-3d-image-slices-into-3d-small-objects/4001)

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**Author:** [@Ali009](https://discourse.itk.org/u/Ali009)\
**Replies:** 1\
**Last updated:** [April 1, 2021, 1:31pm UTC](https://discourse.itk.org/t/split-crop-3d-image-slices-into-3d-small-objects/4001 "2021-04-01T13:31:19Z")

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Hi. I have grayscale images 720x720x300(image size where 300 slices of 3d image). To generate more examples from available data i cropped the images into multiple small objects. But i just use WxH and i need Z too. I don…

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## [JPEG 2000 Part 2 and Multicomponent images](https://discourse.itk.org/t/jpeg-2000-part-2-and-multicomponent-images/3994)

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**Author:** [@agirault](https://discourse.itk.org/u/agirault)\
**Replies:** 3\
**Last updated:** [April 1, 2021, 8:32am UTC](https://discourse.itk.org/t/jpeg-2000-part-2-and-multicomponent-images/3994 "2021-04-01T08:32:07Z")

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I’m attempting to generate test DICOM data in all the supported transfer syntaxes that PACS systems could send to a service consuming DICOM: http://dicom.nema.org/medical/dicom/current/output/chtml/part18/sect\_8.7.3.htm…

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## [Reading 2d png image stack to 3d volume rendering](https://discourse.itk.org/t/reading-2d-png-image-stack-to-3d-volume-rendering/3914)

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**Author:** [@Saptarshi\_Paul](https://discourse.itk.org/u/Saptarshi_Paul)\
**Replies:** 3\
**Last updated:** [March 29, 2021, 1:40pm UTC](https://discourse.itk.org/t/reading-2d-png-image-stack-to-3d-volume-rendering/3914 "2021-03-29T13:40:16Z")

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Hello Everyone, I am new to itk.js and volume rendering as a whole. I was able to create a 3d volume from 2d png image stack in vtk python. Now i want to run the same thing in vtk.js and use itk.js to read the image sta…

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## [Writing dicom file through using ImageSeriesReader](https://discourse.itk.org/t/writing-dicom-file-through-using-imageseriesreader/2563)

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**Author:** [@tatsuaki](https://discourse.itk.org/u/tatsuaki)\
**Replies:** 5\
**Last updated:** [March 29, 2021, 12:32pm UTC](https://discourse.itk.org/t/writing-dicom-file-through-using-imageseriesreader/2563 "2021-03-29T12:32:14Z")

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Hi, please help. I cannot write correctly dicom. I did following step, # load L40t1 = "path/to/dcm image dir" series\_IDsT1 = sitk.ImageSeriesReader.GetGDCMSeriesIDs(L40t1) if not series\_IDsT1: print("ERROR: given …

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## [SimpleITK Image registration 4.13 vs 5.1](https://discourse.itk.org/t/simpleitk-image-registration-4-13-vs-5-1/3649)

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**Author:** [@Nick\_Rubert](https://discourse.itk.org/u/Nick_Rubert)\
**Replies:** 8\
**Last updated:** [March 25, 2021, 9:19pm UTC](https://discourse.itk.org/t/simpleitk-image-registration-4-13-vs-5-1/3649 "2021-03-25T21:19:31Z")

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Hi message board, I’ve got some code running in SimpleITK v4.13.1 that I would like to make compatible with SimpleITK 5.1.1. (This is old code that I’m updating to run with Ubuntu 20.0 and the default SimpleITK version …

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## [SimpleITK Pip install of specific version](https://discourse.itk.org/t/simpleitk-pip-install-of-specific-version/3985)

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**Author:** [@Nick\_Rubert](https://discourse.itk.org/u/Nick_Rubert)\
**Replies:** 1\
**Last updated:** [March 25, 2021, 8:11pm UTC](https://discourse.itk.org/t/simpleitk-pip-install-of-specific-version/3985 "2021-03-25T20:11:08Z")

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Hi message board, Is there a command to let me install a specific version of SimpleITK with pip. I would like to install v 1.2.4 because I’m looking for the old registration framework that used discreteGaussianImageFil…

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## [Crash on calling ImageFileReader::New() MSVS 2019](https://discourse.itk.org/t/crash-on-calling-imagefilereader-new-msvs-2019/3984)

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**Author:** [@ljubak](https://discourse.itk.org/u/ljubak)\
**Replies:** 2\
**Last updated:** [March 25, 2021, 3:32pm UTC](https://discourse.itk.org/t/crash-on-calling-imagefilereader-new-msvs-2019/3984 "2021-03-25T15:32:13Z")

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Hello everyone! I have recently compiled ITK on Windows 7 using Community MSVS 2019. Now I am trying to get myself acquainted with ITK and I am trying out to compile the first examples. And immediately I run into a prob…

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## [multi-Grid Bspline Image Registration error](https://discourse.itk.org/t/multi-grid-bspline-image-registration-error/3980)

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**Author:** [@hfeng](https://discourse.itk.org/u/hfeng)\
**Replies:** 6\
**Last updated:** [March 25, 2021, 1:53pm UTC](https://discourse.itk.org/t/multi-grid-bspline-image-registration-error/3980 "2021-03-25T13:53:58Z")

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Hi, I am testing the examples provided officially, DeformableRegistration6.cxx. The first 2 stages went well. But the third stage stopped at step 15 and exited with an error information “Optimizer stop condition = A rou…

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## [Multi-resolution Demons Registration](https://discourse.itk.org/t/multi-resolution-demons-registration/3981)

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**Author:** [@hfeng](https://discourse.itk.org/u/hfeng)\
**Replies:** 0\
**Last updated:** [March 24, 2021, 8:57pm UTC](https://discourse.itk.org/t/multi-resolution-demons-registration/3981 "2021-03-24T20:57:41Z")

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Hi, I am trying to do the deformable image registration using demons, simply extending the example “DeformableRegistration16.cxx” to 3d images. A multi-resolution scheme is used here with 4 levels. Where can I find the …

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## [Unable to use ITK filters when packaging my Python project that lists ITK as a requirement.](https://discourse.itk.org/t/unable-to-use-itk-filters-when-packaging-my-python-project-that-lists-itk-as-a-requirement/3977)

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**Author:** [@joeykleingers](https://discourse.itk.org/u/joeykleingers)\
**Replies:** 1\
**Last updated:** [March 24, 2021, 3:44pm UTC](https://discourse.itk.org/t/unable-to-use-itk-filters-when-packaging-my-python-project-that-lists-itk-as-a-requirement/3977 "2021-03-24T15:44:02Z")

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Hello, I am relatively new to Python and I have a Python project with a requirements.txt file and a setup.py file inside of it. My requirements.txt file has itk listed as a requirement. The code in my setup.py file re…

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## [Anyone registering multi-spectral remote sensing images](https://discourse.itk.org/t/anyone-registering-multi-spectral-remote-sensing-images/3968)

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**Author:** [@Arrigo\_Benedetti](https://discourse.itk.org/u/Arrigo_Benedetti)\
**Replies:** 3\
**Last updated:** [March 24, 2021, 3:07pm UTC](https://discourse.itk.org/t/anyone-registering-multi-spectral-remote-sensing-images/3968 "2021-03-24T15:07:56Z")

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I was wondering if anyone in this forum has ever used ITK/SimpleITK to register hyper spectral satellite imagery. Any advice is very welcome!

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## [Read an fdf file in python](https://discourse.itk.org/t/read-an-fdf-file-in-python/3964)

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**Author:** [@jtduda](https://discourse.itk.org/u/jtduda)\
**Replies:** 4\
**Last updated:** [March 23, 2021, 9:54pm UTC](https://discourse.itk.org/t/read-an-fdf-file-in-python/3964 "2021-03-23T21:54:27Z")

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I’m trying to read an .fdf file in python. I installed the relevant package via: pip install itk-iofdf I then tried the following: import itk from itk import IOFDF x = itk.image\_file\_reader(filename="M0slice002.fdf" )…

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## [Finding unmerged commit](https://discourse.itk.org/t/finding-unmerged-commit/3975)

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**Author:** [@Soren\_Christensen](https://discourse.itk.org/u/Soren_Christensen)\
**Replies:** 4\
**Last updated:** [March 23, 2021, 8:51pm UTC](https://discourse.itk.org/t/finding-unmerged-commit/3975 "2021-03-23T20:51:28Z")

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Hi, I have a problem getting RayCastInterpolateImageFunction to work with ImageRegistrationMethodv4. It works fine if I just attach it to a resampler and use it that way. I see someone had an issue here and Matt McCor…

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## [How to extract labels of connected components?](https://discourse.itk.org/t/how-to-extract-labels-of-connected-components/3469)

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**Author:** [@Enr\_Brunetti](https://discourse.itk.org/u/Enr_Brunetti)\
**Replies:** 3\
**Last updated:** [March 22, 2021, 2:59pm UTC](https://discourse.itk.org/t/how-to-extract-labels-of-connected-components/3469 "2021-03-22T14:59:42Z")

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I have used the itk::ConnectedComponentImageFilter. For each slice I have a certain number of connected component. I want to obtain a label associated to each of these ones, but with the following code I obtain only one …

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## [Drop support for GCC 4.x?](https://discourse.itk.org/t/drop-support-for-gcc-4-x/3874)

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**Author:** [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Replies:** 10\
**Last updated:** [March 19, 2021, 2:27pm UTC](https://discourse.itk.org/t/drop-support-for-gcc-4-x/3874 "2021-03-19T14:27:29Z")

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PR2231 caused a lot of build errors on a nightly machine with GCC 4.8.4. GCC 4.8.4 does not seem to support C++11 well enough for the latest GTest to compile. Should we upgrade the compiler on this machine and say that …

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## [git review-push failing login to GitHub](https://discourse.itk.org/t/git-review-push-failing-login-to-github/3969)

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**Author:** [@rflanz](https://discourse.itk.org/u/rflanz)\
**Replies:** 1\
**Last updated:** [March 18, 2021, 8:50pm UTC](https://discourse.itk.org/t/git-review-push-failing-login-to-github/3969 "2021-03-18T20:50:36Z")

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Hi, I have a fix branch that I would like to submit for pull request. When I issue a git review-push I get the GitHub login dialog, but my credentials do not work and I always get an error to push the branch. I have a…

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## [Where to place bugfix found in 5.1.2 release](https://discourse.itk.org/t/where-to-place-bugfix-found-in-5-1-2-release/3962)

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**Author:** [@rflanz](https://discourse.itk.org/u/rflanz)\
**Replies:** 2\
**Last updated:** [March 17, 2021, 3:06pm UTC](https://discourse.itk.org/t/where-to-place-bugfix-found-in-5-1-2-release/3962 "2021-03-17T15:06:19Z")

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I have found a bug in the 5.1.2 release and wish to make post a fix which I believe should fix the issue. Are there ongoing patch releases for 5.1.2, or is it better to post the fix to the 5.2 release candidate, which l…

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