# Latest

**URL:** https://discourse.itk.org/latest.md?page=72

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

**Page:** 73

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## [Register head CT to common template](https://discourse.itk.org/t/register-head-ct-to-common-template/2787)

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**Author:** [@trypag](https://discourse.itk.org/u/trypag)\
**Replies:** 13\
**Last updated:** [March 6, 2020, 3:33pm UTC](https://discourse.itk.org/t/register-head-ct-to-common-template/2787 "2020-03-06T15:33:20Z")

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Hello, I have a large dataset of head CTs I would like to normalize : 1/ Same size 512x512x40 2/ Same RAI Orientation 3/ Same centering 4/ Same head alignment I have a head CT template that I could use to center an…

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## [How to extract a volume around a voxel in a 3D image?](https://discourse.itk.org/t/how-to-extract-a-volume-around-a-voxel-in-a-3d-image/2768)

<div class="topic-metadata">

**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 15\
**Last updated:** [March 4, 2020, 11:07am UTC](https://discourse.itk.org/t/how-to-extract-a-volume-around-a-voxel-in-a-3d-image/2768 "2020-03-04T11:07:09Z")

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Suppose I have a 3D image of 250\*250\*250 size. I want to extract a volume of 25\*25\*25 around a particular voxel that could be defined by me. Is there any example that I could look into ??

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## [SWIG TypeError when using the python version of ITKIsotropicWavelets](https://discourse.itk.org/t/swig-typeerror-when-using-the-python-version-of-itkisotropicwavelets/2791)

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**Author:** [@joe-from-mtl](https://discourse.itk.org/u/joe-from-mtl)\
**Replies:** 4\
**Last updated:** [March 5, 2020, 11:45pm UTC](https://discourse.itk.org/t/swig-typeerror-when-using-the-python-version-of-itkisotropicwavelets/2791 "2020-03-05T23:45:41Z")

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Hi, I am trying to reproduce the example runRieszWaveletAnalysis from the ITKIsotropicWavelets repository using Python. I installed the package using the pip command. I ran into an error when trying to generate a monoge…

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## [Do segmentation on dicom volume](https://discourse.itk.org/t/do-segmentation-on-dicom-volume/2695)

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**Author:** [@flaviu2](https://discourse.itk.org/u/flaviu2)\
**Replies:** 5\
**Last updated:** [March 5, 2020, 3:53pm UTC](https://discourse.itk.org/t/do-segmentation-on-dicom-volume/2695 "2020-03-05T15:53:19Z")

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I have found some similar post here, but they are not clear me enough, so forgive me if I put here a too simple question. I have a VC++ app that read dicom images (with VTK DICOM library). I am using for that vtkDICOMRe…

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## [Why ITK v 5.0.1 can not find the fuzzy connectedness method?](https://discourse.itk.org/t/why-itk-v-5-0-1-can-not-find-the-fuzzy-connectedness-method/2780)

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**Author:** [@qiang-zhang-neu](https://discourse.itk.org/u/qiang-zhang-neu)\
**Replies:** 3\
**Last updated:** [March 5, 2020, 3:49pm UTC](https://discourse.itk.org/t/why-itk-v-5-0-1-can-not-find-the-fuzzy-connectedness-method/2780 "2020-03-05T15:49:37Z")

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I want to use fuzzy connectedness method in my project. In the network, it shows that the itk::SimpleFuzzyConnectednessScalarImageFilter is available. However, I can not find a itkSimpleFuzzyConnectednessScalarImageFilte…

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## [Effect of setting orientation on CenteredTransformInitializer](https://discourse.itk.org/t/effect-of-setting-orientation-on-centeredtransforminitializer/2786)

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**Author:** [@trypag](https://discourse.itk.org/u/trypag)\
**Replies:** 3\
**Last updated:** [March 5, 2020, 3:43pm UTC](https://discourse.itk.org/t/effect-of-setting-orientation-on-centeredtransforminitializer/2786 "2020-03-05T15:43:23Z")

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Hello, I am a complete beginner in image registration, much more I am lacking experience in debugging and tuning a registration pipeline. Goal : Translate a head CT to the center and rotate based on a CT template image…

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## [ExhaustiveOptimizerv4 missing in python interface](https://discourse.itk.org/t/exhaustiveoptimizerv4-missing-in-python-interface/2764)

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**Author:** [@Pavel\_Smal](https://discourse.itk.org/u/Pavel_Smal)\
**Replies:** 1\
**Last updated:** [March 5, 2020, 3:08am UTC](https://discourse.itk.org/t/exhaustiveoptimizerv4-missing-in-python-interface/2764 "2020-03-05T03:08:19Z")

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I’m using python itk package 5.0.1 from pypi on windows I notices that ExhaustiveOptimizerv4 is missing, only ExhaustiveOptimizer (which is v3) is present. Is that intentional?

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## [SWIG in SimpleITK architecture](https://discourse.itk.org/t/swig-in-simpleitk-architecture/2782)

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**Author:** [@kayarre](https://discourse.itk.org/u/kayarre)\
**Replies:** 5\
**Last updated:** [March 5, 2020, 2:52am UTC](https://discourse.itk.org/t/swig-in-simpleitk-architecture/2782 "2020-03-05T02:52:01Z")

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Can someone point me to the design of how swig is being used in ITK/SimpleITK? Or explain that succinctly in terms of the architecture, merits and limitations? I asked a similar question about vtk not knowing that SWIG …

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## [Container iterators](https://discourse.itk.org/t/container-iterators/2774)

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**Author:** [@Gordian](https://discourse.itk.org/u/Gordian)\
**Replies:** 7\
**Last updated:** [March 4, 2020, 12:35am UTC](https://discourse.itk.org/t/container-iterators/2774 "2020-03-04T00:35:45Z")

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Hello, i would like to know if there is an container iterator that provide the functionality I need for the C++17 features like std::reduce() with an parallel execution policy. This might improve the performance of some…

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## [interpolate stack of images](https://discourse.itk.org/t/interpolate-stack-of-images/2725)

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**Author:** [@kayarre](https://discourse.itk.org/u/kayarre)\
**Replies:** 13\
**Last updated:** [March 3, 2020, 2:57pm UTC](https://discourse.itk.org/t/interpolate-stack-of-images/2725 "2020-03-03T14:57:42Z")

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I have a stack of images where the thickness of each slice is known and there is a gap of known distance between each slice. I have used and seen where image resampling is used to create isotropic volumes from image sli…

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## [Saving non-orthogonal volume in Nifti format](https://discourse.itk.org/t/saving-non-orthogonal-volume-in-nifti-format/2760)

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**Author:** [@lassoan](https://discourse.itk.org/u/lassoan)\
**Replies:** 22\
**Last updated:** [March 3, 2020, 2:55pm UTC](https://discourse.itk.org/t/saving-non-orthogonal-volume-in-nifti-format/2760 "2020-03-03T14:55:58Z")

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When writing a Nifti image, NiftiImageIO seems to silently orthogonalize the IJK to LPS matrix that is written to the file. Is this normalization really necessary? Can nifti store images with non-orthogonal axes? (I’ve…

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## [Binary closing slower than grayscale closing](https://discourse.itk.org/t/binary-closing-slower-than-grayscale-closing/2770)

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**Author:** [@Come](https://discourse.itk.org/u/Come)\
**Replies:** 2\
**Last updated:** [March 2, 2020, 6:56pm UTC](https://discourse.itk.org/t/binary-closing-slower-than-grayscale-closing/2770 "2020-03-02T18:56:18Z")

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Hi, Context : I have a binary input image of type itk::Image\<unsigned char, 2\> (the image is a 512x512 pixels) and I am applying a closing filter on it using a itk::FlatStructuringElement\<2\>. The type of the structuring…

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## [ensuring correct data type of image](https://discourse.itk.org/t/ensuring-correct-data-type-of-image/2767)

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**Author:** [@kayarre](https://discourse.itk.org/u/kayarre)\
**Replies:** 3\
**Last updated:** [February 28, 2020, 4:25am UTC](https://discourse.itk.org/t/ensuring-correct-data-type-of-image/2767 "2020-02-28T04:25:44Z")

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I am creating an image gridImage = sitk.Image(\[2, 2, slices\], sitk.sitkVectorFloat64, 3) then modifying the contents: displacements = sitk.GetArrayFromImage(gridImage) # modify displacements contents displacementImage…

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## [Simple test for SimpleITK to VTK conversion](https://discourse.itk.org/t/simple-test-for-simpleitk-to-vtk-conversion/2752)

<div class="topic-metadata">

**Author:** [@flaviu2](https://discourse.itk.org/u/flaviu2)\
**Replies:** 5\
**Last updated:** [February 27, 2020, 2:40pm UTC](https://discourse.itk.org/t/simple-test-for-simpleitk-to-vtk-conversion/2752 "2020-02-27T14:40:06Z")

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I have tried a simple test to check my conversion from SimpleITK to VTK: // visualize vtkVolume color ... /// convert VTK ro SimpleITK sitk::Image img = importer.Execute(); //////////////////////////////////////////// i…

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## ["Installing" ITK 5](https://discourse.itk.org/t/installing-itk-5/2766)

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**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 5\
**Last updated:** [February 26, 2020, 9:30pm UTC](https://discourse.itk.org/t/installing-itk-5/2766 "2020-02-26T21:30:19Z")

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We are currently using ITK 5.1rc2 for our project. We have noticed that if we just set ITK\_DIR to the build directory for ITK our project will compile. If we do an “install” of ITK into a different directory then set ITK…

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## [accessing pixel value of a point](https://discourse.itk.org/t/accessing-pixel-value-of-a-point/2765)

<div class="topic-metadata">

**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 1\
**Last updated:** [February 26, 2020, 2:09pm UTC](https://discourse.itk.org/t/accessing-pixel-value-of-a-point/2765 "2020-02-26T14:09:08Z")

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I transformed the image from the index to the physical point. Now I want to apply a certain condition to the pointset and set the corresponding pixel value to a new value. I know that we can access or set pixel value t…

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## [how to get the 0-th component for vector image](https://discourse.itk.org/t/how-to-get-the-0-th-component-for-vector-image/2759)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 6\
**Last updated:** [February 26, 2020, 1:08am UTC](https://discourse.itk.org/t/how-to-get-the-0-th-component-for-vector-image/2759 "2020-02-26T01:08:41Z")

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Let’s I have a vector image: using VectorPixelType = itk::Vector\< float, 3\>; using DisplacementFieldType = itk::Image\< VectorPixelType, 3\>; DisplacementFieldType ::Pointer displacementField = DisplacementFieldType ::New…

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## [Compile first simpleitk c++ project for Windows](https://discourse.itk.org/t/compile-first-simpleitk-c-project-for-windows/2683)

<div class="topic-metadata">

**Author:** [@flaviu2](https://discourse.itk.org/u/flaviu2)\
**Replies:** 15\
**Last updated:** [February 25, 2020, 2:52pm UTC](https://discourse.itk.org/t/compile-first-simpleitk-c-project-for-windows/2683 "2020-02-25T14:52:28Z")

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I have successfully compiled SimpleITK library, helped by Git and CMake. I have to make a parentheses: I would like to compile SimpleITK by CMake GUI, to choose what I need and what I not need, but I cannot do that, not …

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## [how to use cmake map\_imported\_config\_\<config\> with ITK](https://discourse.itk.org/t/how-to-use-cmake-map-imported-config-config-with-itk/2734)

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**Author:** [@sghosh](https://discourse.itk.org/u/sghosh)\
**Replies:** 3\
**Last updated:** [February 24, 2020, 1:25pm UTC](https://discourse.itk.org/t/how-to-use-cmake-map-imported-config-config-with-itk/2734 "2020-02-24T13:25:53Z")

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Hello, I am using ITK -3.20.1 version in my own project with visual studio. I would like to create a custom configuration derived from release in this manner: foreach(\_itklib ${ITK\_LIBRARIES}) set\_target\_properties($…

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## [Why sitk.GetDirection() is not the same with '0020|0037' ?](https://discourse.itk.org/t/why-sitk-getdirection-is-not-the-same-with-0020-0037/2755)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 3\
**Last updated:** [February 23, 2020, 2:04am UTC](https://discourse.itk.org/t/why-sitk-getdirection-is-not-the-same-with-0020-0037/2755 "2020-02-23T02:04:28Z")

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In my thought, I think both sitk.GetDirection() and ‘0020|0037’ indicate the patient orientation. However, I find they are different. Firstly, I get the direction: \>\>\> sitkImage = sitk.ReadImage('IM\_0177') \>\>\> sitkImag…

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## [Remote Module Grading/Ranking System Needed](https://discourse.itk.org/t/remote-module-grading-ranking-system-needed/2750)

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**Author:** [@hjmjohnson](https://discourse.itk.org/u/hjmjohnson)\
**Replies:** 5\
**Last updated:** [February 21, 2020, 8:09pm UTC](https://discourse.itk.org/t/remote-module-grading-ranking-system-needed/2750 "2020-02-21T20:09:50Z")

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Background One of the primary goals of creating remote modules was to ease the burden of core developers in maintaining the core ITK code base. There are currently 44 remote modules distributed with ITK, but there is n…

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## [The information in SimpleITK is different from that in dicom header](https://discourse.itk.org/t/the-information-in-simpleitk-is-different-from-that-in-dicom-header/2737)

<div class="topic-metadata">

**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 12\
**Last updated:** [February 21, 2020, 4:26pm UTC](https://discourse.itk.org/t/the-information-in-simpleitk-is-different-from-that-in-dicom-header/2737 "2020-02-21T16:26:17Z")

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I am using SimpleITK in my project, and I find the patient position read by SimpleITK is differaent from that from dicom header (RadiAnt). Firstly, I use image = sitk.ReadImage(names) to read image, and I am quite sure …

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## [Updating a sub region in ImageToVTKImageFilter](https://discourse.itk.org/t/updating-a-sub-region-in-imagetovtkimagefilter/702)

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**Author:** [@benjaminhon](https://discourse.itk.org/u/benjaminhon)\
**Replies:** 16\
**Last updated:** [February 20, 2020, 3:29pm UTC](https://discourse.itk.org/t/updating-a-sub-region-in-imagetovtkimagefilter/702 "2020-02-20T15:29:45Z")

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Hi all, I am performing some annotation functions which which modifies the ITK image -\> ImageToVTKImageFilter -\> vtkImageViewer2. However, this is quite slow for large images because I need to call ImageToVTKImageFilte…

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## [Question of the pipeline of MultiResolutionPDEDeformableRegistration](https://discourse.itk.org/t/question-of-the-pipeline-of-multiresolutionpdedeformableregistration/2749)

<div class="topic-metadata">

**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 2\
**Last updated:** [February 20, 2020, 3:00pm UTC](https://discourse.itk.org/t/question-of-the-pipeline-of-multiresolutionpdedeformableregistration/2749 "2020-02-20T15:00:31Z")

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Currently, I need to use GPU based Demons on my project. Unfortunately, the GPU based Demons don’t work for multi-resolution framework. Thus, I implement myself multi-resolution code for GPU based Demons. My code is: #i…

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## [static compiled example exits with segfault](https://discourse.itk.org/t/static-compiled-example-exits-with-segfault/2744)

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**Author:** [@Vincent](https://discourse.itk.org/u/Vincent)\
**Replies:** 3\
**Last updated:** [February 20, 2020, 11:41am UTC](https://discourse.itk.org/t/static-compiled-example-exits-with-segfault/2744 "2020-02-20T11:41:06Z")

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Dear members, as I am quite new to ITK, I hope someone can help me out with this static runtime crash. I am trying to statically compile an example from ITK to the statix ITK libraries. make build dir mkdir itk-stati…

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## [GPU version Demons: the size of output is different from that of input image](https://discourse.itk.org/t/gpu-version-demons-the-size-of-output-is-different-from-that-of-input-image/2743)

<div class="topic-metadata">

**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 1\
**Last updated:** [February 20, 2020, 1:53am UTC](https://discourse.itk.org/t/gpu-version-demons-the-size-of-output-is-different-from-that-of-input-image/2743 "2020-02-20T01:53:10Z")

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I am using GPU Demons for myself project. I find a strange bug: the size of input (fix and moving image) is (174, 256, 256), but the size of output is (87, 128, 128). The main code is: RegistrationFilterType::Pointer …

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## [Zenodo citation author ORCID iD's and affiliations](https://discourse.itk.org/t/zenodo-citation-author-orcid-ids-and-affiliations/2746)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 0\
**Last updated:** [February 19, 2020, 6:05pm UTC](https://discourse.itk.org/t/zenodo-citation-author-orcid-ids-and-affiliations/2746 "2020-02-19T18:05:27Z")

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Hi folks, We now have a Zenodo record for ITK :tada: . For more information on Zenodo, see https://help.zenodo.org/features/. This enables publications to cite a specific version of ITK, which is important for reproduci…

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## [Bug for GPU Demons](https://discourse.itk.org/t/bug-for-gpu-demons/2740)

<div class="topic-metadata">

**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 1\
**Last updated:** [February 19, 2020, 2:09pm UTC](https://discourse.itk.org/t/bug-for-gpu-demons/2740 "2020-02-19T14:09:26Z")

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I want to use GPU Demons in my application with multi-resolution framework. However, the current multi-resolution framework do not suport GPU Demons, thus I implement it by myself. The main code is: using VectorPixelT…

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## [Speeding up Point to Point registration](https://discourse.itk.org/t/speeding-up-point-to-point-registration/2711)

<div class="topic-metadata">

**Author:** [@ShaneKirkbride](https://discourse.itk.org/u/ShaneKirkbride)\
**Replies:** 6\
**Last updated:** [February 19, 2020, 2:00pm UTC](https://discourse.itk.org/t/speeding-up-point-to-point-registration/2711 "2020-02-19T14:00:00Z")

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I have set up a point to point registration. My meshes have about 30K points so this is taking a long time. What should I do to speed this up? Are there any GPU options? I have a GPU and will use the AWS GPU EC2 as well. …

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## [Deformable Registration and .vtk file Help](https://discourse.itk.org/t/deformable-registration-and-vtk-file-help/2699)

<div class="topic-metadata">

**Author:** [@ShaneKirkbride](https://discourse.itk.org/u/ShaneKirkbride)\
**Replies:** 12\
**Last updated:** [February 19, 2020, 1:54pm UTC](https://discourse.itk.org/t/deformable-registration-and-vtk-file-help/2699 "2020-02-19T13:54:18Z")

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I have a set of similar DICOM files. I need to convert them to a 3D mesh and then register them. Then I need to transform the meshes so they are both on the same coordinate system. After this I need to calculate the area…

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