# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=10

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

**Page:** 11

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## [Creating Digitally Reconstructed Radiographs from Chest CT](https://discourse.itk.org/t/creating-digitally-reconstructed-radiographs-from-chest-ct/5801)

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**Author:** [@BraveDistribution](https://discourse.itk.org/u/BraveDistribution)\
**Replies:** 10\
**Last updated:** [March 29, 2023, 11:34am UTC](https://discourse.itk.org/t/creating-digitally-reconstructed-radiographs-from-chest-ct/5801 "2023-03-29T11:34:13Z")

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Hello all, I want to solve a 3D (CT) - 2D (fluoro/xray) registration task. I have found out so far that the most straightforward option is to first generate DRR based on CT and then register them. I am not sure how a g…

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## [Co-registration of more than two images](https://discourse.itk.org/t/co-registration-of-more-than-two-images/5836)

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**Author:** [@avigotsky](https://discourse.itk.org/u/avigotsky)\
**Replies:** 2\
**Last updated:** [March 28, 2023, 11:34pm UTC](https://discourse.itk.org/t/co-registration-of-more-than-two-images/5836 "2023-03-28T23:34:12Z")

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Hi, all, This this may a better question for #algorithms, but since I am new to ITK/SimpleITK, I will ask it here. Suppose I have three images—X, Y, and Z—that I want to register into the same space. I do not have a te…

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## [How to co-register mask on neuroimage generated from RTStruct dicom file?](https://discourse.itk.org/t/how-to-co-register-mask-on-neuroimage-generated-from-rtstruct-dicom-file/5825)

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**Author:** [@Sunita\_Patel](https://discourse.itk.org/u/Sunita_Patel)\
**Replies:** 4\
**Last updated:** [March 27, 2023, 1:58pm UTC](https://discourse.itk.org/t/how-to-co-register-mask-on-neuroimage-generated-from-rtstruct-dicom-file/5825 "2023-03-27T13:58:54Z")

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Dear Simple ITK Team, We have two DICOM series and two RTSTRUCT masks which are converted into Nifti files. The original dimension of the nifti files are (256, 256, 216). We are trying to do registration and resampling …

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## [CMake says TBB version incompatible with ITK installed via conda/mamba](https://discourse.itk.org/t/cmake-says-tbb-version-incompatible-with-itk-installed-via-conda-mamba/5771)

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**Author:** [@KrisThielemans](https://discourse.itk.org/u/KrisThielemans)\
**Replies:** 7\
**Last updated:** [March 25, 2023, 11:08am UTC](https://discourse.itk.org/t/cmake-says-tbb-version-incompatible-with-itk-installed-via-conda-mamba/5771 "2023-03-25T11:08:23Z")

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Hi I installed ITK on a Windows 10 machine via mamba create -n pvc install petpvc libitk-devel (petpvc requires libitk). I then used (non-Conda) CMake 3.25.2 (and VS 2022) to try and build PETPVC sources. After settin…

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## [Applying a transform from .tfm file in ITK](https://discourse.itk.org/t/applying-a-transform-from-tfm-file-in-itk/5566)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 5\
**Last updated:** [December 13, 2022, 2:59pm UTC](https://discourse.itk.org/t/applying-a-transform-from-tfm-file-in-itk/5566 "2022-12-13T14:59:08Z")

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Hi, I have a transform file in.tfm format that was created with 3D-slicer (attached it here for further reference). Now I’d like to read it from ITK and apply it to a specific point as in the example as in the example b…

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## [Transform of points using Euler3DTransform](https://discourse.itk.org/t/transform-of-points-using-euler3dtransform/5830)

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**Author:** [@jm\_nc](https://discourse.itk.org/u/jm_nc)\
**Replies:** 3\
**Last updated:** [March 24, 2023, 12:47pm UTC](https://discourse.itk.org/t/transform-of-points-using-euler3dtransform/5830 "2023-03-24T12:47:35Z")

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Hey Everyone - simple question from a newbie, I’m using simple ITK. I know the registration transform between two (nifti) volumes - I did it manually in MITK and have read back in the offset and rotation. Then I created…

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## [Apply deformation field on source image to get the target image](https://discourse.itk.org/t/apply-deformation-field-on-source-image-to-get-the-target-image/5821)

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**Author:** [@Xinyue](https://discourse.itk.org/u/Xinyue)\
**Replies:** 1\
**Last updated:** [March 22, 2023, 5:45pm UTC](https://discourse.itk.org/t/apply-deformation-field-on-source-image-to-get-the-target-image/5821 "2023-03-22T17:45:24Z")

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Hi all, I am working on generating my own data, I have the deformation fired and the source image, and try to generate the target image. I found somewhere mentioned that it should be done with DisplacementFieldTransform…

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## [Is WarpImageFilter supposed to reverse a displacement field?](https://discourse.itk.org/t/is-warpimagefilter-supposed-to-reverse-a-displacement-field/5819)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 4\
**Last updated:** [March 22, 2023, 3:14pm UTC](https://discourse.itk.org/t/is-warpimagefilter-supposed-to-reverse-a-displacement-field/5819 "2023-03-22T15:14:14Z")

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Continuing the discussion from How to create a displacement field image from a numpy array without files?: Is WarpImageFilter supposed to reverse a displacement field? Hi! I just figured how to warp an image with a disp…

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## [How to create a displacement field image from a numpy array without files?](https://discourse.itk.org/t/how-to-create-a-displacement-field-image-from-a-numpy-array-without-files/5717)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 1\
**Last updated:** [March 22, 2023, 10:53am UTC](https://discourse.itk.org/t/how-to-create-a-displacement-field-image-from-a-numpy-array-without-files/5717 "2023-03-22T10:53:17Z")

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Continuing the discussion from Creating a displacement field image from a numpy array: Hello! I am trying to warp an image. The image is built from an array, and I would like to build the displacement field from anothe…

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## [Setting Up Basic ITK Implementation in Vue 3.x](https://discourse.itk.org/t/setting-up-basic-itk-implementation-in-vue-3-x/5804)

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**Author:** [@davidshq](https://discourse.itk.org/u/davidshq)\
**Replies:** 1\
**Last updated:** [March 15, 2023, 6:38pm UTC](https://discourse.itk.org/t/setting-up-basic-itk-implementation-in-vue-3-x/5804 "2023-03-15T18:38:12Z")

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I ran into some challenges setting up a Vue 3.x project with ITK-wasm and VTK.js. I’ve created a branch of my current project I’m going to leave as a really basic example of a working Vue 3.x project using both ITK-wasm …

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## [Crop patch out of an image](https://discourse.itk.org/t/crop-patch-out-of-an-image/5784)

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**Author:** [@User0](https://discourse.itk.org/u/User0)\
**Replies:** 13\
**Last updated:** [March 14, 2023, 8:17am UTC](https://discourse.itk.org/t/crop-patch-out-of-an-image/5784 "2023-03-14T08:17:26Z")

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I’m trying to use itk (not sitk) to crop out a patch of another image. I have two images A and B that are overlapping, but don’t share the same size, spacing or image origin. Image A is basically a 224x224 square patch.…

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## [How to use cmake fetchcontent to download itk and it's devedent projects?](https://discourse.itk.org/t/how-to-use-cmake-fetchcontent-to-download-itk-and-its-devedent-projects/5785)

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**Author:** [@BlackCat\_Ruelle](https://discourse.itk.org/u/BlackCat_Ruelle)\
**Replies:** 4\
**Last updated:** [March 7, 2023, 10:03pm UTC](https://discourse.itk.org/t/how-to-use-cmake-fetchcontent-to-download-itk-and-its-devedent-projects/5785 "2023-03-07T22:03:32Z")

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Hi, I am new to ITK. I am trying to use cmake to download ITK source code and build my projects. By it gives me strange error: “CMake Error at CMakeLists.txt:18 (include): include called with wrong number of arguments.…

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## [HausdorffDistance on an image with multiple Labels](https://discourse.itk.org/t/hausdorffdistance-on-an-image-with-multiple-labels/4582)

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**Author:** [@toladner](https://discourse.itk.org/u/toladner)\
**Replies:** 6\
**Last updated:** [March 2, 2023, 1:15pm UTC](https://discourse.itk.org/t/hausdorffdistance-on-an-image-with-multiple-labels/4582 "2023-03-02T13:15:09Z")

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I’m evaluating the predictions of a lung lobe segmentation model using the HausdorffDistanceImageFilter. Thus, I’m passing the ground truth and the prediction (both have equal size with 6 labels) into the image filter. …

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## [Mismatched dimensions error](https://discourse.itk.org/t/mismatched-dimensions-error/5773)

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**Author:** [@xxbilian](https://discourse.itk.org/u/xxbilian)\
**Replies:** 1\
**Last updated:** [March 1, 2023, 2:17pm UTC](https://discourse.itk.org/t/mismatched-dimensions-error/5773 "2023-03-01T14:17:32Z")

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Hello, I have a segmentation image of a main image. however, when I try to open the segmentation image on top of the main image, I received an error, “mismatched dimensions”. the main image dimension is 300, 450, 450, w…

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## [What is the use of mesh?](https://discourse.itk.org/t/what-is-the-use-of-mesh/5758)

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**Author:** [@rohit\_inippully](https://discourse.itk.org/u/rohit_inippully)\
**Replies:** 1\
**Last updated:** [February 27, 2023, 4:21pm UTC](https://discourse.itk.org/t/what-is-the-use-of-mesh/5758 "2023-02-27T16:21:41Z")

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I just started with Itk tutorials. I am wondering what is the practical use of mesh and different types of cells? Thanks in advance.

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## [SimpleITK: Registration working but applying the transform to a single point does not](https://discourse.itk.org/t/simpleitk-registration-working-but-applying-the-transform-to-a-single-point-does-not/5728)

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**Author:** [@Bouthros](https://discourse.itk.org/u/Bouthros)\
**Replies:** 6\
**Last updated:** [February 24, 2023, 11:58pm UTC](https://discourse.itk.org/t/simpleitk-registration-working-but-applying-the-transform-to-a-single-point-does-not/5728 "2023-02-24T23:58:20Z")

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Hi! I hope I am putting this question in the proper category. I followed the Jupyter notebook concerning the 3D registration and I tried to apply it to my problem. Here is my problem: I have 2 axial series, 1 fixed an…

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## [how to solve "Error:exception occured during image IO"?](https://discourse.itk.org/t/how-to-solve-error-exception-occured-during-image-io/5740)

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**Author:** [@yuliang\_zhang](https://discourse.itk.org/u/yuliang_zhang)\
**Replies:** 1\
**Last updated:** [February 22, 2023, 2:38pm UTC](https://discourse.itk.org/t/how-to-solve-error-exception-occured-during-image-io/5740 "2023-02-22T14:38:15Z")

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when i try open a series of dicom ultrasound image,it shows this error,what’s wrong?

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

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**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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