# Latest

**URL:** https://discourse.itk.org/latest.md?page=57

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

**Page:** 58

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## [How to speed up for 3D filtering](https://discourse.itk.org/t/how-to-speed-up-for-3d-filtering/3719)

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**Author:** [@buyierfei](https://discourse.itk.org/u/buyierfei)\
**Replies:** 8\
**Last updated:** [December 21, 2020, 4:17pm UTC](https://discourse.itk.org/t/how-to-speed-up-for-3d-filtering/3719 "2020-12-21T16:17:59Z")

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I found it such slow that using built-in 3D filtering method directly. For example, I want to implement mean filtering in a 3D image data, which size is 1024 \* 1024 \* 1024, and I use itkMeanImageFilter method, but it sea…

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## [How to set non-uniform spacing](https://discourse.itk.org/t/how-to-set-non-uniform-spacing/3715)

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**Author:** [@Anesh](https://discourse.itk.org/u/Anesh)\
**Replies:** 2\
**Last updated:** [December 21, 2020, 3:06pm UTC](https://discourse.itk.org/t/how-to-set-non-uniform-spacing/3715 "2020-12-21T15:06:47Z")

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Hello, I am reading in 2D multislice MRI data which contains e.g. 3 slices using the SetImportPointer for registration. The Z-slices are positioned at -101.25, -33.75 and -18.75 mm. I am confused on how to use the image…

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## [Unsupported compiler error when linking with Intel compiler](https://discourse.itk.org/t/unsupported-compiler-error-when-linking-with-intel-compiler/3709)

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**Author:** [@Fijoy\_Vadakkumpadan](https://discourse.itk.org/u/Fijoy_Vadakkumpadan)\
**Replies:** 3\
**Last updated:** [December 17, 2020, 9:24pm UTC](https://discourse.itk.org/t/unsupported-compiler-error-when-linking-with-intel-compiler/3709 "2020-12-17T21:24:39Z")

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Hello, I successfully built ITK 5.1.1 static libraries with gcc 7.4, but having an issue linking them to my application, which uses an Intel compiler. I’m getting an “Unsupported compiler” error thrown by the generated…

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## [Universal Windows Platform](https://discourse.itk.org/t/universal-windows-platform/3713)

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**Author:** [@skn123](https://discourse.itk.org/u/skn123)\
**Replies:** 1\
**Last updated:** [December 17, 2020, 8:59pm UTC](https://discourse.itk.org/t/universal-windows-platform/3713 "2020-12-17T20:59:23Z")

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Is there any mechanism to build ITK with UWP rather than a pure Win32 build? I tried force-fitting it with specific tags and various files failed to compile.

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## [OrientedGaussianInterpolateImageFilter Python ITK](https://discourse.itk.org/t/orientedgaussianinterpolateimagefilter-python-itk/3708)

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**Author:** [@Nick\_Rubert](https://discourse.itk.org/u/Nick_Rubert)\
**Replies:** 2\
**Last updated:** [December 17, 2020, 8:43pm UTC](https://discourse.itk.org/t/orientedgaussianinterpolateimagefilter-python-itk/3708 "2020-12-17T20:43:43Z")

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Hi message board, I’m trying to port some code from Python ITK v 4.13.0 to Python wrapped ITK v 5.1.1 or SimpleITK \`\`\` 2.0.0 (ITK 5.1). In ITK v 4.13 I’m using the OrientedGaussianInterpolateImageFilter to simulate bl…

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## [Translate ITK DeformableRegistration15.cxx into SimpleITK](https://discourse.itk.org/t/translate-itk-deformableregistration15-cxx-into-simpleitk/3691)

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**Author:** [@cdcooke](https://discourse.itk.org/u/cdcooke)\
**Replies:** 3\
**Last updated:** [December 16, 2020, 2:44pm UTC](https://discourse.itk.org/t/translate-itk-deformableregistration15-cxx-into-simpleitk/3691 "2020-12-16T14:44:41Z")

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Greetings! Has anyone tried converting the ITK DeformableRegistration15.cxx example for use with SimpleITK? There are several calls in the DeformableRegistration15.cxx that I can’t seem to map into SimpleITK. Any help…

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## [Help displaying a 3D Dicom and the corresponding segmentation Slicewise using itkwidgets](https://discourse.itk.org/t/help-displaying-a-3d-dicom-and-the-corresponding-segmentation-slicewise-using-itkwidgets/3507)

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**Author:** [@Kashyap](https://discourse.itk.org/u/Kashyap)\
**Replies:** 6\
**Last updated:** [December 15, 2020, 10:01pm UTC](https://discourse.itk.org/t/help-displaying-a-3d-dicom-and-the-corresponding-segmentation-slicewise-using-itkwidgets/3507 "2020-12-15T22:01:01Z")

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I am able to display the 3D Dicom read using simple ITK and also overlay the corresponding segmentation mesh in vtkpolydata format. Now I am trying to display the same image slice wise (kind of like an extension of the …

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## [CMake Error](https://discourse.itk.org/t/cmake-error/3705)

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**Author:** [@Afzaal786-wq](https://discourse.itk.org/u/Afzaal786-wq)\
**Replies:** 1\
**Last updated:** [December 15, 2020, 9:40pm UTC](https://discourse.itk.org/t/cmake-error/3705 "2020-12-15T21:40:16Z")

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Hello hope you doing well, I have installed ITK 5.1.2 successfully for Gate 9.0 installation. But during configuration of ITK i got this error even file ITKConfig.cmake is present in ITK5.1.2/bin. CMake Error at CMakeLi…

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## [Registering vertebra CT and MRI](https://discourse.itk.org/t/registering-vertebra-ct-and-mri/3694)

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**Author:** [@Ray\_Jian](https://discourse.itk.org/u/Ray_Jian)\
**Replies:** 6\
**Last updated:** [December 11, 2020, 1:42am UTC](https://discourse.itk.org/t/registering-vertebra-ct-and-mri/3694 "2020-12-11T01:42:52Z")

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Hello, All. I am trying to register vertebra in spine CT and MRI. The average size of the vertebra MRI is (200-300, 100-200, 15). The average number of intensity in MRI is around 500. Which is calculated by this. min\_…

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## [cmpiling ITK on CentOs - pcre/swig error](https://discourse.itk.org/t/cmpiling-itk-on-centos-pcre-swig-error/3673)

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**Author:** [@Yaron](https://discourse.itk.org/u/Yaron)\
**Replies:** 5\
**Last updated:** [December 10, 2020, 9:56pm UTC](https://discourse.itk.org/t/cmpiling-itk-on-centos-pcre-swig-error/3673 "2020-12-10T21:56:59Z")

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Hello, I am trying to compile ITK on a CentOs 7 cluster. During the compilation, I get the error - \[ 56%\] Completed ‘PCRE’ \[ 56%\] Built target PCRE … \[ 56%\] No update step for ‘swig’ \[ 56%\] No patch step for ‘swig’ …

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## [creating an GPU image from a pointer](https://discourse.itk.org/t/creating-an-gpu-image-from-a-pointer/3696)

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**Author:** [@agerardin](https://discourse.itk.org/u/agerardin)\
**Replies:** 0\
**Last updated:** [December 10, 2020, 5:43pm UTC](https://discourse.itk.org/t/creating-an-gpu-image-from-a-pointer/3696 "2020-12-10T17:43:22Z")

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Is it possible to provide an existing pointer to unified memory and create a GPUImage? I am managing my data through another library but I would like to leverage some of the nice 3D processing ITK provides.

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## [How to extract the region](https://discourse.itk.org/t/how-to-extract-the-region/3687)

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**Author:** [@buyierfei](https://discourse.itk.org/u/buyierfei)\
**Replies:** 5\
**Last updated:** [December 10, 2020, 2:26pm UTC](https://discourse.itk.org/t/how-to-extract-the-region/3687 "2020-12-10T14:26:41Z")

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I am a beginner. I use the connected component analysis method to extract the labels of a volume data. How can I use any one of the labels as a mask to extract the corresponding area in the original data? Which header fi…

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## [Generalized dicom series reader](https://discourse.itk.org/t/generalized-dicom-series-reader/3692)

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**Author:** [@Hasna](https://discourse.itk.org/u/Hasna)\
**Replies:** 2\
**Last updated:** [December 10, 2020, 2:59am UTC](https://discourse.itk.org/t/generalized-dicom-series-reader/3692 "2020-12-10T02:59:56Z")

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Hi, I am trying to write a generalized reader code for dicom series. To get the component type of the data i am reading first dicom file of the series and using dicomIO-\>GetComponentType() .This will give whether the …

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## [Research associate/postdoc position](https://discourse.itk.org/t/research-associate-postdoc-position/3693)

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**Author:** [@ntustison](https://discourse.itk.org/u/ntustison)\
**Replies:** 0\
**Last updated:** [December 9, 2020, 8:32pm UTC](https://discourse.itk.org/t/research-associate-postdoc-position/3693 "2020-12-09T20:32:42Z")

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Research associate/postdoc starting from May 1 2021 for a year. Requirement: PhD in Engineering or Science with 0-3 years of experience in image processing. Prior experience in working with medical image data is a plus.…

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## [RegistrationV4 and BsplineTransform Parallellization](https://discourse.itk.org/t/registrationv4-and-bsplinetransform-parallellization/3683)

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**Author:** [@machadoL](https://discourse.itk.org/u/machadoL)\
**Replies:** 4\
**Last updated:** [December 8, 2020, 9:34pm UTC](https://discourse.itk.org/t/registrationv4-and-bsplinetransform-parallellization/3683 "2020-12-08T21:34:28Z")

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Hello everyone. As I’ve been mentioning in my previous posts, I am working in a deformable registration pipeline. It happens that I am running my tests in a supercomputer and noticed that the code I wrote using ITK cla…

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## [ITK 5.1.2 has been released!](https://discourse.itk.org/t/itk-5-1-2-has-been-released/3688)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 0\
**Last updated:** [December 8, 2020, 5:35pm UTC](https://discourse.itk.org/t/itk-5-1-2-has-been-released/3688 "2020-12-08T17:35:53Z")

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We are happy to announce the Insight Toolkit (ITK) 5.1.2! :tada: ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration. Python Packages Install ITK …

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## [Patches for ITK 5.1.2](https://discourse.itk.org/t/patches-for-itk-5-1-2/3635)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 16\
**Last updated:** [December 8, 2020, 5:30pm UTC](https://discourse.itk.org/t/patches-for-itk-5-1-2/3635 "2020-12-08T17:30:17Z")

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Hi folks, The next patch (bugfix) release, ITK 5.1.2, is coming up. Patches currently staged on the Git release branch are: Bradley Lowekamp (4): COMP: Updating ITKSimpleITKFilters remote module BUG: Addre…

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## [Creating a displacement field image from a numpy array](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681)

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**Author:** [@Alex\_Reimelt](https://discourse.itk.org/u/Alex_Reimelt)\
**Replies:** 11\
**Last updated:** [December 8, 2020, 5:06pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681 "2020-12-08T17:06:18Z")

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Hello, in my PhD project I analyze 3D microCT datasets of lung tissue samples to find out more about the alveolar shape. One topic is the simulation of an atelectasis by warping the image. In order to do that (using the…

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## [Create ITK Setup project](https://discourse.itk.org/t/create-itk-setup-project/3678)

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**Author:** [@James](https://discourse.itk.org/u/James)\
**Replies:** 3\
**Last updated:** [December 5, 2020, 6:25pm UTC](https://discourse.itk.org/t/create-itk-setup-project/3678 "2020-12-05T18:25:06Z")

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Hi, I’m new here. I downloaded ITK 5.1.1 for Windows, configured, generated using CMake successfully, and Compiled successfully on Visual Studio 2019. When I trying to create installation project got error: Building …

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## [Interpolate between slices or remove segmentation outlier](https://discourse.itk.org/t/interpolate-between-slices-or-remove-segmentation-outlier/3666)

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**Author:** [@farhan\_009](https://discourse.itk.org/u/farhan_009)\
**Replies:** 3\
**Last updated:** [December 1, 2020, 2:22pm UTC](https://discourse.itk.org/t/interpolate-between-slices-or-remove-segmentation-outlier/3666 "2020-12-01T14:22:04Z")

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Hello Everyone, I have the following output from the prediction of the deep learning model. Is there any function that interpolates the segmented result of I have to remove the dots? I have tried to use the LinearInter…

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## [speed up registration process](https://discourse.itk.org/t/speed-up-registration-process/3667)

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**Author:** [@pierrectl](https://discourse.itk.org/u/pierrectl)\
**Replies:** 2\
**Last updated:** [December 1, 2020, 9:25am UTC](https://discourse.itk.org/t/speed-up-registration-process/3667 "2020-12-01T09:25:27Z")

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hello everyone, I currently develop a registration algorithm using itk framework. Everything seems to work well, except that execution time is very long, especially metric computation (as expected). I have one question:…

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## [LBFGS optimizer](https://discourse.itk.org/t/lbfgs-optimizer/3658)

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**Author:** [@pierrectl](https://discourse.itk.org/u/pierrectl)\
**Replies:** 3\
**Last updated:** [December 1, 2020, 9:24am UTC](https://discourse.itk.org/t/lbfgs-optimizer/3658 "2020-12-01T09:24:47Z")

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hello everyone, I was wondering if itk developers provided a registration example between two 3d images using LBFGS optimizer ? I already checked test examples and program throws the following exception when computing r…

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## [using the itk : GeodesicActiveContour](https://discourse.itk.org/t/using-the-itk-geodesicactivecontour/3642)

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**Author:** [@abir](https://discourse.itk.org/u/abir)\
**Replies:** 5\
**Last updated:** [November 30, 2020, 5:32pm UTC](https://discourse.itk.org/t/using-the-itk-geodesicactivecontour/3642 "2020-11-30T17:32:31Z")

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I used the MRI dataset provided by Left Atrial Segmentation Challenge 2013which was part of the STACOM’13 workshop this is the data I used test\_data training\_data I am suppose to segment the left atrium wall (epicrdi…

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## [How to read dicom files in two folders by SimpleITK?](https://discourse.itk.org/t/how-to-read-dicom-files-in-two-folders-by-simpleitk/3663)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 2\
**Last updated:** [November 30, 2020, 4:10am UTC](https://discourse.itk.org/t/how-to-read-dicom-files-in-two-folders-by-simpleitk/3663 "2020-11-30T04:10:10Z")

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SimpleITK is a useful tool for medical image processing. It can read dicom images by: import SimpleITK as sitk series\_IDs = sitk.ImageSeriesReader.GetGDCMSeriesIDs(file\_path) series\_file\_names = sitk.ImageSeriesReade…

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## [How can i read a dicom file in “float pixel format”, using "itkConnectedThresholdImageFilter" and write it to dicom file again?](https://discourse.itk.org/t/how-can-i-read-a-dicom-file-in-float-pixel-format-using-itkconnectedthresholdimagefilter-and-write-it-to-dicom-file-again/2971)

<div class="topic-metadata">

**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 0\
**Last updated:** [April 19, 2020, 4:01am UTC](https://discourse.itk.org/t/how-can-i-read-a-dicom-file-in-float-pixel-format-using-itkconnectedthresholdimagefilter-and-write-it-to-dicom-file-again/2971 "2020-04-19T04:01:25Z")

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I test as next, but failed: typedef float InternalOneFilePixelType; const unsigned int DimensionOneFile = 2; typedef itk::Image\< InternalOneFilePixelType, DimensionOneFile \> InternalOneFileImageTy…

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## [Slice to Volume registration](https://discourse.itk.org/t/slice-to-volume-registration/3659)

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**Author:** [@aabbcc](https://discourse.itk.org/u/aabbcc)\
**Replies:** 3\
**Last updated:** [November 28, 2020, 2:06pm UTC](https://discourse.itk.org/t/slice-to-volume-registration/3659 "2020-11-28T14:06:35Z")

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I have a 3D microCT image about a tissue sample. And I use a ultramicrotome to get some ultrathin sections(slices) of the tissue. Then I get these slices’ 2D images using electron microscope. How can I use itk to registe…

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## [Troble loading and reading LinearTransform.h5](https://discourse.itk.org/t/troble-loading-and-reading-lineartransform-h5/3008)

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**Author:** [@machadoL](https://discourse.itk.org/u/machadoL)\
**Replies:** 9\
**Last updated:** [November 28, 2020, 1:45am UTC](https://discourse.itk.org/t/troble-loading-and-reading-lineartransform-h5/3008 "2020-11-28T01:45:55Z")

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Hello, everyone. I am implementing a pipeline to load a LinearTransform.h5 and convert that into a displacement field. However, I am having a problem loading the transform into a real transform object-pointer to proceed…

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## [No outputs from view(image) of itkwidgets](https://discourse.itk.org/t/no-outputs-from-view-image-of-itkwidgets/3657)

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**Author:** [@Satya](https://discourse.itk.org/u/Satya)\
**Replies:** 5\
**Last updated:** [November 28, 2020, 1:09am UTC](https://discourse.itk.org/t/no-outputs-from-view-image-of-itkwidgets/3657 "2020-11-28T01:09:30Z")

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When I run the following lines from the jupyter notebook provided as examples on github in my system, I fail to get any outputs : image = itk.imread(file\_name) view(image) I have checked everything from the package ve…

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## [linker error while invoking "make" command in my ITK's build directory](https://discourse.itk.org/t/linker-error-while-invoking-make-command-in-my-itks-build-directory/3652)

<div class="topic-metadata">

**Author:** [@Nayra\_Ahmed](https://discourse.itk.org/u/Nayra_Ahmed)\
**Replies:** 3\
**Last updated:** [November 27, 2020, 3:52pm UTC](https://discourse.itk.org/t/linker-error-while-invoking-make-command-in-my-itks-build-directory/3652 "2020-11-27T15:52:25Z")

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Hi all, I got the below error when I invoke the make command in ITK’s build directory. clang: \*\*error:\*\* linker command failed with exit code 1 (use -v to see invocation) make\[2\]: \*\*\* \[bin/libitktiff.3.20.1.dylib\] Erro…

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## [itk::ERROR Image(0x55f0ab8f5690): A spacing of 0 is not allowed: Spacing is \[0, 0, 0\]](https://discourse.itk.org/t/itk-error-image-0x55f0ab8f5690-a-spacing-of-0-is-not-allowed-spacing-is-0-0-0/3648)

<div class="topic-metadata">

**Author:** [@machadoL](https://discourse.itk.org/u/machadoL)\
**Replies:** 3\
**Last updated:** [November 26, 2020, 4:41pm UTC](https://discourse.itk.org/t/itk-error-image-0x55f0ab8f5690-a-spacing-of-0-is-not-allowed-spacing-is-0-0-0/3648 "2020-11-26T16:41:23Z")

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Hello, everyone! I am struggling with that error: itk::ERROR Image(0x55f0ab8f5690): A spacing of 0 is not allowed: Spacing is \[0, 0, 0\] The situation is the following: I am performing a multistage image registration. …

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