# Latest

**URL:** https://discourse.itk.org/latest.md?page=27

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

**Page:** 28

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## [Registration: Dimensional Differences in Images, Padding](https://discourse.itk.org/t/registration-dimensional-differences-in-images-padding/5723)

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**Author:** [@elapins](https://discourse.itk.org/u/elapins)\
**Replies:** 3\
**Last updated:** [February 18, 2023, 6:43pm UTC](https://discourse.itk.org/t/registration-dimensional-differences-in-images-padding/5723 "2023-02-18T18:43:34Z")

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How does ITK/SimpleITK account for dimensional differences between images during registration?? OR do they need to be padded accordingly?

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## [Affine Transform: Offset vs. fixed center](https://discourse.itk.org/t/affine-transform-offset-vs-fixed-center/5721)

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**Author:** [@elapins](https://discourse.itk.org/u/elapins)\
**Replies:** 2\
**Last updated:** [February 18, 2023, 4:12pm UTC](https://discourse.itk.org/t/affine-transform-offset-vs-fixed-center/5721 "2023-02-18T16:12:39Z")

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When initializing an affine transform for a registration framework, what is the difference between the offset and the fixed center inputs?

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## [SimpleITK Registration](https://discourse.itk.org/t/simpleitk-registration/5709)

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**Author:** [@elapins](https://discourse.itk.org/u/elapins)\
**Replies:** 2\
**Last updated:** [February 17, 2023, 9:10pm UTC](https://discourse.itk.org/t/simpleitk-registration/5709 "2023-02-17T21:10:28Z")

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Hello, I have been trying to implement a SimpleITK registration framework to register a reference image that has no change with a deformed image (warped image). I split the reference image up into subregions and try to…

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## [No ROI available for itkwidgets.view when using 3D glyphs](https://discourse.itk.org/t/no-roi-available-for-itkwidgets-view-when-using-3d-glyphs/5716)

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**Author:** [@Kevin\_Sweeney](https://discourse.itk.org/u/Kevin_Sweeney)\
**Replies:** 0\
**Last updated:** [February 17, 2023, 3:33pm UTC](https://discourse.itk.org/t/no-roi-available-for-itkwidgets-view-when-using-3d-glyphs/5716 "2023-02-17T15:33:02Z")

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I am not seeing an option to select a region of interest for my data. I am unsure as to whether that is as expected. It works when trying the example: itkwidgets/SelectRegionOfInterest.ipynb at master · InsightSoftwareC…

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## [Saving LabelOverlay Image as DICOM series](https://discourse.itk.org/t/saving-labeloverlay-image-as-dicom-series/5689)

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**Author:** [@Franciska](https://discourse.itk.org/u/Franciska)\
**Replies:** 10\
**Last updated:** [February 17, 2023, 5:12am UTC](https://discourse.itk.org/t/saving-labeloverlay-image-as-dicom-series/5689 "2023-02-17T05:12:06Z")

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Hi! I have a DICOM series, and with the segmentations I create a LabelOverlay Image. When I write it out as a DICOM series, I modified the following datatags in the created image, to get an RGB image.: image\_slice.Se…

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## [Creating mask from rtstruct](https://discourse.itk.org/t/creating-mask-from-rtstruct/3826)

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**Author:** [@roirodriguez](https://discourse.itk.org/u/roirodriguez)\
**Replies:** 4\
**Last updated:** [February 16, 2023, 5:45pm UTC](https://discourse.itk.org/t/creating-mask-from-rtstruct/3826 "2023-02-16T17:45:57Z")

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Hi, I’m just beginning with SimpleITK and all other medical image related software. I’m actually loading some dicom series and their corresponding RTSTRUCT contours in python, manually with numpy, because as far as i kn…

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## [Labelmap to scaler](https://discourse.itk.org/t/labelmap-to-scaler/5693)

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**Author:** [@Sean\_Hatton](https://discourse.itk.org/u/Sean_Hatton)\
**Replies:** 4\
**Last updated:** [February 15, 2023, 5:46pm UTC](https://discourse.itk.org/t/labelmap-to-scaler/5693 "2023-02-15T17:46:26Z")

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How do you get a labelmap back to a scalar image? I have been trying the below, but I keep getting a labelmap with on object, not a scalar. LabelmapToBinary didn’t work. Thoughts? I am trying to run mrc2tif but it won’t …

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## [ITK compile: failed to open file H5make\_libsetting.exe](https://discourse.itk.org/t/itk-compile-failed-to-open-file-h5make-libsetting-exe/5707)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 1\
**Last updated:** [February 15, 2023, 2:30pm UTC](https://discourse.itk.org/t/itk-compile-failed-to-open-file-h5make-libsetting-exe/5707 "2023-02-15T14:30:36Z")

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I am compiling ITK from source code, and it reports a bug for release version: can not open file "D:\\ITK\\build\\bin\\Release\\H5make\_libsettings.ext" But the compiling is OK for debug version. The environment is: ITK 5.…

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## [How do I use a \`vtkStructuredGrid\`?](https://discourse.itk.org/t/how-do-i-use-a-vtkstructuredgrid/5705)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 0\
**Last updated:** [February 14, 2023, 5:14pm UTC](https://discourse.itk.org/t/how-do-i-use-a-vtkstructuredgrid/5705 "2023-02-14T17:14:41Z")

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Hello, I would like to know if there is a way to cast, filter or otherwise load a vtkStructuredGrid with ITK? (something similar to itk.image\_from\_vtk\_image would be great, but any other way is welcome). Thanks! | itk …

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## [Using swig on external standalone libraries that use ITK](https://discourse.itk.org/t/using-swig-on-external-standalone-libraries-that-use-itk/345)

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**Author:** [@nslay](https://discourse.itk.org/u/nslay)\
**Replies:** 3\
**Last updated:** [February 13, 2023, 9:20pm UTC](https://discourse.itk.org/t/using-swig-on-external-standalone-libraries-that-use-itk/345 "2023-02-13T21:20:06Z")

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Hello Insight-Users, I’ve studied the WrapITK CMake modules and an old wiki describing how to wrap external modules, but I’ve yet to see anything obvious about wrapping a standalone library that uses ITK. Since ITK is a…

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## [sitk.WriteImage to multiple png files](https://discourse.itk.org/t/sitk-writeimage-to-multiple-png-files/5701)

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**Author:** [@Sean\_Hatton](https://discourse.itk.org/u/Sean_Hatton)\
**Replies:** 3\
**Last updated:** [February 13, 2023, 6:25pm UTC](https://discourse.itk.org/t/sitk-writeimage-to-multiple-png-files/5701 "2023-02-13T18:25:38Z")

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I can write a 3d sitk Image to a single png, is there a hidden switch to get multiple pngs per 3D image? Cheers, Sean Hatton, PhD UCSD

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## [How to manipulate itksnap workspace file(.itksnap) via itksnap command line tool (itksnap-wt)?](https://discourse.itk.org/t/how-to-manipulate-itksnap-workspace-file-itksnap-via-itksnap-command-line-tool-itksnap-wt/5699)

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**Author:** [@Sterben\_01](https://discourse.itk.org/u/Sterben_01)\
**Replies:** 1\
**Last updated:** [February 13, 2023, 3:49pm UTC](https://discourse.itk.org/t/how-to-manipulate-itksnap-workspace-file-itksnap-via-itksnap-command-line-tool-itksnap-wt/5699 "2023-02-13T15:49:58Z")

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Hi! I want to manipulate itksnap workspace file(.itksnap) via itksnap command line tool (itksnap-wt). The first step is try to add another .nrrd image in to a workspace file. I trid this command: itksnap-wt -i 1only.i…

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## [Extract Head Scan From CT Angiogram](https://discourse.itk.org/t/extract-head-scan-from-ct-angiogram/5698)

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**Author:** [@niruta](https://discourse.itk.org/u/niruta)\
**Replies:** 4\
**Last updated:** [February 13, 2023, 4:26am UTC](https://discourse.itk.org/t/extract-head-scan-from-ct-angiogram/5698 "2023-02-13T04:26:46Z")

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I want to extract head data from a CT Angiogram which contains the neck scan as well. Is there any way to do this ? This is how the data looks.

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## [(Segmentation fault.) Is it possible to use a single data set with integers (double) as the fixed and moving inputs for registration?](https://discourse.itk.org/t/segmentation-fault-is-it-possible-to-use-a-single-data-set-with-integers-double-as-the-fixed-and-moving-inputs-for-registration/5690)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 2\
**Last updated:** [February 12, 2023, 3:22pm UTC](https://discourse.itk.org/t/segmentation-fault-is-it-possible-to-use-a-single-data-set-with-integers-double-as-the-fixed-and-moving-inputs-for-registration/5690 "2023-02-12T15:22:41Z")

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Hi. I’m getting a segmentation fault. I’m almost sure that I must be messing something up. In summary, I want to check if using a single data set as both moving and fixed images can be registered. I tried the same with f…

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## [CenteredTransformInitializer with only TranslationTransform?](https://discourse.itk.org/t/centeredtransforminitializer-with-only-translationtransform/4635)

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**Author:** [@sdbonte](https://discourse.itk.org/u/sdbonte)\
**Replies:** 2\
**Last updated:** [February 11, 2023, 1:20pm UTC](https://discourse.itk.org/t/centeredtransforminitializer-with-only-translationtransform/4635 "2023-02-11T13:20:10Z")

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I am trying to register two 3D CT scans using SimpleITK. After checking they have the same orientation, I load them from .nii.gz files. Then they look like this (central axial slice displayed): Fixed image: Moving im…

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## [z-maps for comparing PET images](https://discourse.itk.org/t/z-maps-for-comparing-pet-images/5414)

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**Author:** [@Keyn34](https://discourse.itk.org/u/Keyn34)\
**Replies:** 7\
**Last updated:** [February 10, 2023, 9:51pm UTC](https://discourse.itk.org/t/z-maps-for-comparing-pet-images/5414 "2023-02-10T21:51:59Z")

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Hello all, I am trying to compute z-maps for PET images to test it as a comparison methodology/metric with SimpleITK on Python. The formula is simple, but I always have a completely black image with an insanely broad (…

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## [Hello Wasm World!](https://discourse.itk.org/t/hello-wasm-world/5617)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 0\
**Last updated:** [January 9, 2023, 4:19am UTC](https://discourse.itk.org/t/hello-wasm-world/5617 "2023-01-09T04:19:12Z")

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In modern computing, the Web Platform has transformed web browsers into a powerful and accessible application interface. Applications built on open web standards work, with no installation, across operating system and ha…

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## [Create Elegant C++ Spatial Processing Pipelines in WebAssembly](https://discourse.itk.org/t/create-elegant-c-spatial-processing-pipelines-in-webassembly/5692)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 0\
**Last updated:** [February 10, 2023, 9:08pm UTC](https://discourse.itk.org/t/create-elegant-c-spatial-processing-pipelines-in-webassembly/5692 "2023-02-10T21:08:17Z")

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By: Matt McCormick , Mary Elise Dedicke , Henry Schreiner , WebAssembly’s origins date back to Alon Zakai’s incredible effort to build C++ to JavaScript. In 2015, we demonstrated the power of this technology to make sci…

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## [Write mesh data (cell data) with python - it is not working?](https://discourse.itk.org/t/write-mesh-data-cell-data-with-python-it-is-not-working/5682)

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**Author:** [@tutti](https://discourse.itk.org/u/tutti)\
**Replies:** 6\
**Last updated:** [February 10, 2023, 1:19am UTC](https://discourse.itk.org/t/write-mesh-data-cell-data-with-python-it-is-not-working/5682 "2023-02-10T01:19:45Z")

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Hi guys, I’m trying to write the mesh data with point and cell data using python (based on C++). This is my Python codes: from itk import BinaryMask3DMeshSource MeshType = itk.Mesh\[itk.F, 3\] ImageType = itk.Image\[itk…

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## [How do I load a vtkImageData as an image?](https://discourse.itk.org/t/how-do-i-load-a-vtkimagedata-as-an-image/5686)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 0\
**Last updated:** [February 8, 2023, 11:23pm UTC](https://discourse.itk.org/t/how-do-i-load-a-vtkimagedata-as-an-image/5686 "2023-02-08T23:23:44Z")

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Hello, I have been trying to reuse the array of a UniformGrid (PyVista’s equivalent to vtkImageData) with ITK. The resulting data seems to be cropped by 1 voxel. How can I load the data as cells with ITK? (Extra.) Ult…

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## [Blank result with non-default variance for the Gaussian smoothing filter GPU implementation](https://discourse.itk.org/t/blank-result-with-non-default-variance-for-the-gaussian-smoothing-filter-gpu-implementation/5479)

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**Author:** [@Mumumia](https://discourse.itk.org/u/Mumumia)\
**Replies:** 4\
**Last updated:** [February 9, 2023, 2:39pm UTC](https://discourse.itk.org/t/blank-result-with-non-default-variance-for-the-gaussian-smoothing-filter-gpu-implementation/5479 "2023-02-09T14:39:15Z")

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Hi experts, We have implemented the GPU-supported Gaussian smoothing filter. It works ok for the default variance and kernelWidth. However, when changing the variance parameter to a user-specified value, the GPU version…

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## [two label map registration. Bad results.](https://discourse.itk.org/t/two-label-map-registration-bad-results/5670)

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**Author:** [@banikr](https://discourse.itk.org/u/banikr)\
**Replies:** 16\
**Last updated:** [February 8, 2023, 11:07pm UTC](https://discourse.itk.org/t/two-label-map-registration-bad-results/5670 "2023-02-08T23:07:55Z")

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I have a mask that has 2 labels. I want to register it on a segmentation map that has 3 labels(both cases background 0). I have run the following method but getting bad result outputs: mask\_itk = sitk.GetImageFromA…

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## [One example needs to be renamed (Create another instance of a filter?)](https://discourse.itk.org/t/one-example-needs-to-be-renamed-create-another-instance-of-a-filter/5680)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 5\
**Last updated:** [February 8, 2023, 7:19pm UTC](https://discourse.itk.org/t/one-example-needs-to-be-renamed-create-another-instance-of-a-filter/5680 "2023-02-08T19:19:28Z")

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Hi, may be you are already aware, but one of the examples may need to be renamed: https://examples.itk.org/src/core/common/createanother/documentation Its summary is “Copy/duplicate a filter”, so, I assume that it shou…

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## [Funding opportunity: "Advances in Artificial Intelligence to Generate AIMI Annotations"](https://discourse.itk.org/t/funding-opportunity-advances-in-artificial-intelligence-to-generate-aimi-annotations/5685)

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**Author:** [@fedorov](https://discourse.itk.org/u/fedorov)\
**Replies:** 0\
**Last updated:** [February 8, 2023, 5:06pm UTC](https://discourse.itk.org/t/funding-opportunity-advances-in-artificial-intelligence-to-generate-aimi-annotations/5685 "2023-02-08T17:06:42Z")

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Do you have expertise using AI tools for automated annotation of cancer imaging data? Put those to work annotating data in NCI Imaging Data Commons and get funding to do this! See the details at the funding opportunity…

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## [Saving DICOM Series](https://discourse.itk.org/t/saving-dicom-series/5684)

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**Author:** [@Franciska](https://discourse.itk.org/u/Franciska)\
**Replies:** 5\
**Last updated:** [February 8, 2023, 3:26pm UTC](https://discourse.itk.org/t/saving-dicom-series/5684 "2023-02-08T15:26:38Z")

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Hello! I am reading in a DICOM series with SimpleITK. If I save this as a nii.gz file, it shows up perfectly in Slicer, however if I try to save it as a DICOM series, based on this example code, the DICOM series shows up…

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## [CT-MRI registration: Error when initialising images centre](https://discourse.itk.org/t/ct-mri-registration-error-when-initialising-images-centre/5651)

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**Author:** [@Priscilla](https://discourse.itk.org/u/Priscilla)\
**Replies:** 6\
**Last updated:** [February 7, 2023, 12:13pm UTC](https://discourse.itk.org/t/ct-mri-registration-error-when-initialising-images-centre/5651 "2023-02-07T12:13:28Z")

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Hello, I’m at the beginning of registering CT and MRI dicom files of the thorax, and I’m stuck on the part of finding the centre of the images. I get the following error message: RuntimeError: Exception thrown in Simpl…

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## [About multilevel registration](https://discourse.itk.org/t/about-multilevel-registration/5675)

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**Author:** [@ma1282029525](https://discourse.itk.org/u/ma1282029525)\
**Replies:** 0\
**Last updated:** [February 6, 2023, 2:14am UTC](https://discourse.itk.org/t/about-multilevel-registration/5675 "2023-02-06T02:14:23Z")

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At the time of registration, I chose two levels of registration to speed up the registration using the image pyramid. But after the first level of registration, I almost got the correct results, but the second level of r…

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## [Transformation translation error?](https://discourse.itk.org/t/transformation-translation-error/5673)

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**Author:** [@Matthieu\_Brucher](https://discourse.itk.org/u/Matthieu_Brucher)\
**Replies:** 0\
**Last updated:** [February 4, 2023, 6:59pm UTC](https://discourse.itk.org/t/transformation-translation-error/5673 "2023-02-04T18:59:22Z")

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I’m trying to use the example from Register Image to Another Using Landmarks — v5.3.0 to set up a registration based on matching set of points. The estimated transform seems to me OK: AffineTransform (0x157604c30) RTTI…

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## [How to separate channels from a NRRD file?](https://discourse.itk.org/t/how-to-separate-channels-from-a-nrrd-file/5671)

<div class="topic-metadata">

**Author:** [@Sterben\_01](https://discourse.itk.org/u/Sterben_01)\
**Replies:** 2\
**Last updated:** [February 3, 2023, 3:23pm UTC](https://discourse.itk.org/t/how-to-separate-channels-from-a-nrrd-file/5671 "2023-02-03T15:23:52Z")

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Hi! I am a beginner of ITK/VTK. Currently, I have an NRRD file, and it has three channels. If I want to separate it and write it to three files, which class should I use? I know how to read and write, but I don’t know h…

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## [Squeeze dicom from 4D to 3D in C#](https://discourse.itk.org/t/squeeze-dicom-from-4d-to-3d-in-c/5668)

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**Author:** [@Endian](https://discourse.itk.org/u/Endian)\
**Replies:** 1\
**Last updated:** [February 2, 2023, 2:16pm UTC](https://discourse.itk.org/t/squeeze-dicom-from-4d-to-3d-in-c/5668 "2023-02-02T14:16:15Z")

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Is there a way to reshape a 4D sitk image to 3D e.g. \[256, 256, 256, 1\] to \[256, 256, 256\] in C#? In python it is done with slicing: image = image\[:,:,:,0\] How is this done in C#?

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