# Latest

**URL:** https://discourse.itk.org/latest.md?page=44

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

**Page:** 45

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## [Where can I learn theory necessary for SimpleITK](https://discourse.itk.org/t/where-can-i-learn-theory-necessary-for-simpleitk/4567)

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**Author:** [@aryamansriram](https://discourse.itk.org/u/aryamansriram)\
**Replies:** 2\
**Last updated:** [November 10, 2021, 3:41pm UTC](https://discourse.itk.org/t/where-can-i-learn-theory-necessary-for-simpleitk/4567 "2021-11-10T15:41:33Z")

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Hi, I am an absolute beginner when it comes to ITK and I am tasked with performing a fairly complex image registration task ( Registration of thermal images ). I ran a few example notebooks within the repo and I wanted t…

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## [Should ScalarImageToCooccurrenceMatrixFilter have a template parameter for the mask image type?](https://discourse.itk.org/t/should-scalarimagetocooccurrencematrixfilter-have-a-template-parameter-for-the-mask-image-type/4562)

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**Author:** [@emmenlau](https://discourse.itk.org/u/emmenlau)\
**Replies:** 2\
**Last updated:** [November 9, 2021, 2:27pm UTC](https://discourse.itk.org/t/should-scalarimagetocooccurrencematrixfilter-have-a-template-parameter-for-the-mask-image-type/4562 "2021-11-09T14:27:26Z")

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Currently ScalarImageToCooccurrenceMatrixFilter assumes that the mask image would be the same type as the gray value image. This is not ideal, and can be even problematic when working with floating-point types. I think …

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## [Interpolate a given point from nifti DVF image volume](https://discourse.itk.org/t/interpolate-a-given-point-from-nifti-dvf-image-volume/4543)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 7\
**Last updated:** [November 9, 2021, 2:19pm UTC](https://discourse.itk.org/t/interpolate-a-given-point-from-nifti-dvf-image-volume/4543 "2021-11-09T14:19:09Z")

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I have extracted a mesh points from a given nifti image which has a dimension of (203, 127, 161). Additionally, I have a deformation vector field as an another nifti file which is generated using the aforementioned 3D n…

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## [Texture for all objects with labeled images](https://discourse.itk.org/t/texture-for-all-objects-with-labeled-images/4554)

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**Author:** [@emmenlau](https://discourse.itk.org/u/emmenlau)\
**Replies:** 6\
**Last updated:** [November 9, 2021, 9:53am UTC](https://discourse.itk.org/t/texture-for-all-objects-with-labeled-images/4554 "2021-11-09T09:53:54Z")

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I would like to compute texture statistics on a gray value image, but separately for image regions that are given in a separate label image. Basically the same as itk::LabelStatisticsImageFilter\<RawImage, LabelImage\> doe…

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## [MIP in 3 directions](https://discourse.itk.org/t/mip-in-3-directions/4559)

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**Author:** [@Aleena\_Suhail](https://discourse.itk.org/u/Aleena_Suhail)\
**Replies:** 1\
**Last updated:** [November 8, 2021, 1:47pm UTC](https://discourse.itk.org/t/mip-in-3-directions/4559 "2021-11-08T13:47:03Z")

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How can I generated MIP of brain mra in 3 directions xyz using simpleitk

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## [Range indexing an ITK image by variables](https://discourse.itk.org/t/range-indexing-an-itk-image-by-variables/4557)

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**Author:** [@sedghi](https://discourse.itk.org/u/sedghi)\
**Replies:** 2\
**Last updated:** [November 8, 2021, 3:16am UTC](https://discourse.itk.org/t/range-indexing-an-itk-image-by-variables/4557 "2021-11-08T03:16:01Z")

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I’m trying to slice an sitk image in 3D but having trouble. The following code doesn’t work for some reason Does not work image = sitk.ReadImage('./myImage.nrrd') i\_indices = np.arange(100,164) // or range(100,164) j\_i…

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## [How to dilate a 3D label image while keeping its' original label values?](https://discourse.itk.org/t/how-to-dilate-a-3d-label-image-while-keeping-its-original-label-values/4550)

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**Author:** [@andieku](https://discourse.itk.org/u/andieku)\
**Replies:** 4\
**Last updated:** [November 5, 2021, 10:51pm UTC](https://discourse.itk.org/t/how-to-dilate-a-3d-label-image-while-keeping-its-original-label-values/4550 "2021-11-05T22:51:30Z")

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Hi, I am trying to use SimpleITK in Python to dilate all non-zero regions in a 3D label image while keeping the image’s original label values. I tried following this Multi-label Morphology example but sitk.Morphological…

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## [Applying a 4x4 affine transform to a 3D volume](https://discourse.itk.org/t/applying-a-4x4-affine-transform-to-a-3d-volume/4555)

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**Author:** [@joeykleingers](https://discourse.itk.org/u/joeykleingers)\
**Replies:** 3\
**Last updated:** [November 5, 2021, 7:17pm UTC](https://discourse.itk.org/t/applying-a-4x4-affine-transform-to-a-3d-volume/4555 "2021-11-05T19:17:40Z")

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I am trying to apply a 4x4 affine transform to a 3D volume to rotate the volume 1 degree along the Y-axis. This is a very simple example that I am trying to prove works so that I can use a more complicated 4x4 transform…

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## [Proposal to improve ITK factory registration CMake infrastructure](https://discourse.itk.org/t/proposal-to-improve-itk-factory-registration-cmake-infrastructure/4546)

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**Author:** [@jcfr](https://discourse.itk.org/u/jcfr)\
**Replies:** 3\
**Last updated:** [November 5, 2021, 6:46pm UTC](https://discourse.itk.org/t/proposal-to-improve-itk-factory-registration-cmake-infrastructure/4546 "2021-11-05T18:46:26Z")

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Summary The key idea of the proposal linked below was to introduce a CMake function called itk\_configure\_factory allowing to associate relevant properties to CMake targets. Ultimately, for each target, this function wil…

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## [Resampling difference between SimpleITK and scipy's zoom](https://discourse.itk.org/t/resampling-difference-between-simpleitk-and-scipys-zoom/4548)

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**Author:** [@couzulli](https://discourse.itk.org/u/couzulli)\
**Replies:** 2\
**Last updated:** [November 4, 2021, 7:16pm UTC](https://discourse.itk.org/t/resampling-difference-between-simpleitk-and-scipys-zoom/4548 "2021-11-04T19:16:20Z")

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I am checking a simple resampling operation to double the size of input array. SimpleITK’s resample output seems to be shifted to left and top by one voxel. Is there any other argument such as origin of the grid that I n…

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## [Image Registration of binary images](https://discourse.itk.org/t/image-registration-of-binary-images/2911)

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**Author:** [@Felippe\_Trigueiro\_An](https://discourse.itk.org/u/Felippe_Trigueiro_An)\
**Replies:** 3\
**Last updated:** [November 3, 2021, 6:28am UTC](https://discourse.itk.org/t/image-registration-of-binary-images/2911 "2021-11-03T06:28:52Z")

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HI guys, I’d like to register two binary brain images. I tried to use the MSE, correlation and MI in the SimpleITK but the result was not so good, so what metric do you suggest? I think that I need a metric which compare…

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## [In Python, how to convert between SimpleITK and ITK Images?](https://discourse.itk.org/t/in-python-how-to-convert-between-simpleitk-and-itk-images/1922)

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**Author:** [@alkamid](https://discourse.itk.org/u/alkamid)\
**Replies:** 5\
**Last updated:** [November 2, 2021, 2:43pm UTC](https://discourse.itk.org/t/in-python-how-to-convert-between-simpleitk-and-itk-images/1922 "2021-11-02T14:43:05Z")

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There is a C++ tutorial on how to convert between SimpleITK and ITK, but I’m struggling to translate it into Python. In \[14\]: test\_arr = np.ones((30, 30, 30), dtype=np.int16) In \[…

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## [Is there a function for High and Lowpass filtering in SITK?](https://discourse.itk.org/t/is-there-a-function-for-high-and-lowpass-filtering-in-sitk/4541)

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**Author:** [@kolibril13](https://discourse.itk.org/u/kolibril13)\
**Replies:** 4\
**Last updated:** [November 2, 2021, 12:59pm UTC](https://discourse.itk.org/t/is-there-a-function-for-high-and-lowpass-filtering-in-sitk/4541 "2021-11-02T12:59:30Z")

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Is there any Filter to manipulate the frequency domain of an image/stack in sitk? I could not find one here: https://simpleitk.readthedocs.io/en/master/filters.html I am working with 3D data, and it would be amazing i…

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## [Trying to access LabelGeometryImageFilter in ITK 5.2.1.post1 python package.](https://discourse.itk.org/t/trying-to-access-labelgeometryimagefilter-in-itk-5-2-1-post1-python-package/4538)

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**Author:** [@LalithShiyam](https://discourse.itk.org/u/LalithShiyam)\
**Replies:** 5\
**Last updated:** [November 1, 2021, 7:38pm UTC](https://discourse.itk.org/t/trying-to-access-labelgeometryimagefilter-in-itk-5-2-1-post1-python-package/4538 "2021-11-01T19:38:14Z")

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Dear ITK devs, Many thanks for creating such a solid tool. I am currently trying to migrate from SimpleITK to ITK python because of LabelGeometryImageFilter’s ability to calculate orientation as well. I would like to ca…

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## [Reading, Filtering and Writing in multiple threads](https://discourse.itk.org/t/reading-filtering-and-writing-in-multiple-threads/4503)

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**Author:** [@Keyn34](https://discourse.itk.org/u/Keyn34)\
**Replies:** 3\
**Last updated:** [October 30, 2021, 1:56pm UTC](https://discourse.itk.org/t/reading-filtering-and-writing-in-multiple-threads/4503 "2021-10-30T13:56:02Z")

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Hello everyone ( again :D), Are there any resources or tips on running a function like this void multiStaple(std::vector\<std::string\> inputfiles) { // itk::MultiLabelSTAPLEImageFilter Type FilterType::Pointer …

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## [creating a 2D projection image from a 3D array (extracted from a single DICOM series)](https://discourse.itk.org/t/creating-a-2d-projection-image-from-a-3d-array-extracted-from-a-single-dicom-series/4532)

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**Author:** [@Marcelo\_Straus\_Takah](https://discourse.itk.org/u/Marcelo_Straus_Takah)\
**Replies:** 1\
**Last updated:** [October 29, 2021, 3:51pm UTC](https://discourse.itk.org/t/creating-a-2d-projection-image-from-a-3d-array-extracted-from-a-single-dicom-series/4532 "2021-10-29T15:51:59Z")

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Hello all. Please forgive me if this question has already been asked, I have searched but did not find anything similar. I have a 3D head CT series in DICOM format and would like to generate multiple 2D images of a 3D …

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## [Issue installing ITKPythonPackage with pip](https://discourse.itk.org/t/issue-installing-itkpythonpackage-with-pip/4530)

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**Author:** [@ClaraJ](https://discourse.itk.org/u/ClaraJ)\
**Replies:** 1\
**Last updated:** [October 28, 2021, 1:00pm UTC](https://discourse.itk.org/t/issue-installing-itkpythonpackage-with-pip/4530 "2021-10-28T13:00:15Z")

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Hi, I need itk 5.2 so I am trying to install itk python packages with pip. I am running a windows 10 64bit, python 3.7 within anaconda3 environment, Microsoft Visual Studio 2019. After installing pypi, cmake 3.21 & sci…

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## [Image index ordering in Python API](https://discourse.itk.org/t/image-index-ordering-in-python-api/4496)

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**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 7\
**Last updated:** [October 27, 2021, 9:03pm UTC](https://discourse.itk.org/t/image-index-ordering-in-python-api/4496 "2021-10-27T21:03:47Z")

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I know this topic has been discussed before, and maybe all decisions have been made and too much legacy exists anyway already… Still, I find it strange to have this numpy array like view of an ITK image with inverted in…

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## [Type annotations and itk.Image\[...\]](https://discourse.itk.org/t/type-annotations-and-itk-image/4407)

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**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 10\
**Last updated:** [October 27, 2021, 1:08pm UTC](https://discourse.itk.org/t/type-annotations-and-itk-image/4407 "2021-10-27T13:08:30Z")

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I am writing some Python code built on itk and other packages. Many of the methods take itk images as arguments. What is the best way add type annotations for itk images? In most cases I don’t care about the pixel type …

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## [Slicing operation of VTK or ITK in C++](https://discourse.itk.org/t/slicing-operation-of-vtk-or-itk-in-c/4509)

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**Author:** [@buyierfei](https://discourse.itk.org/u/buyierfei)\
**Replies:** 2\
**Last updated:** [October 27, 2021, 8:23pm UTC](https://discourse.itk.org/t/slicing-operation-of-vtk-or-itk-in-c/4509 "2021-10-27T20:23:22Z")

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In C++, does the ITK or VTK volume data class contain a numpy-like slicing method?

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## [MetaIO image rotation conventions](https://discourse.itk.org/t/metaio-image-rotation-conventions/4525)

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**Author:** [@ingmar.voigt](https://discourse.itk.org/u/ingmar.voigt)\
**Replies:** 6\
**Last updated:** [October 27, 2021, 3:38pm UTC](https://discourse.itk.org/t/metaio-image-rotation-conventions/4525 "2021-10-27T15:38:11Z")

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For the TransformMatrix / Orientation / Rotation tags - which are storing the image rotation in the MetaIO (MHD/MHA) format - the actual serialization convention (row-major vs. column major) does not seem to be documente…

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## [CLAHE implementation on ITK](https://discourse.itk.org/t/clahe-implementation-on-itk/4486)

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**Author:** [@diaferiaroberta](https://discourse.itk.org/u/diaferiaroberta)\
**Replies:** 3\
**Last updated:** [October 27, 2021, 3:16pm UTC](https://discourse.itk.org/t/clahe-implementation-on-itk/4486 "2021-10-27T15:16:54Z")

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There is a way to use the Karel Zuiderveld CLAHE algorithm on ITK? The only available function is itk::AdaptiveHistogramEqualizationImageFilter, but for my image has poor results. I’m working with an image that has doub…

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## [Particle swarm optimization in image](https://discourse.itk.org/t/particle-swarm-optimization-in-image/4464)

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**Author:** [@Jonas](https://discourse.itk.org/u/Jonas)\
**Replies:** 1\
**Last updated:** [October 27, 2021, 1:16pm UTC](https://discourse.itk.org/t/particle-swarm-optimization-in-image/4464 "2021-10-27T13:16:22Z")

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Hi, I would like to experiment with Particle swarm optimization to see if I can retrieve some vessels centerlines from the sum of the paths of PSO particles. The ITK implementation seems to work only to find minimums, …

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## [Unexpected Behavior of LinearInterpolateImageFunction](https://discourse.itk.org/t/unexpected-behavior-of-linearinterpolateimagefunction/4450)

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**Author:** [@krm15](https://discourse.itk.org/u/krm15)\
**Replies:** 4\
**Last updated:** [October 27, 2021, 12:53pm UTC](https://discourse.itk.org/t/unexpected-behavior-of-linearinterpolateimagefunction/4450 "2021-10-27T12:53:14Z")

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Here is an example of using the LineageInterpolateImageFunction from the ITKSphinxExamples repository: https://itk.org/ITKExamples/src/Core/ImageFunction/LinearlyInterpolatePositionInImage/Documentation.html In this ex…

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## [How to pass output memory to a filter (avoid a copy to external memory)?](https://discourse.itk.org/t/how-to-pass-output-memory-to-a-filter-avoid-a-copy-to-external-memory/4501)

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**Author:** [@emmenlau](https://discourse.itk.org/u/emmenlau)\
**Replies:** 10\
**Last updated:** [October 26, 2021, 7:07pm UTC](https://discourse.itk.org/t/how-to-pass-output-memory-to-a-filter-avoid-a-copy-to-external-memory/4501 "2021-10-26T19:07:10Z")

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We use ITK together with a lot of older code that has its own memory management. It was quite easy to wrap our memory containers into an itk::Image using itk::ImportImageFilter. It was also very straightforward to apply …

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## [SimpleITK ExhaustiveOptimizerv4 Error](https://discourse.itk.org/t/simpleitk-exhaustiveoptimizerv4-error/4516)

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**Author:** [@yarzh](https://discourse.itk.org/u/yarzh)\
**Replies:** 1\
**Last updated:** [October 26, 2021, 3:20pm UTC](https://discourse.itk.org/t/simpleitk-exhaustiveoptimizerv4-error/4516 "2021-10-26T15:20:11Z")

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Hello, I am trying to use ExhaustiveOptimizer to find a good-ish initial displacement field transform between multimodal 2D images. But it looks like it is impossible to assign Optimizer Scales in any way. I’ve tried R…

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## [MIP](https://discourse.itk.org/t/mip/4521)

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**Author:** [@Aleena\_Suhail](https://discourse.itk.org/u/Aleena_Suhail)\
**Replies:** 11\
**Last updated:** [October 25, 2021, 9:29pm UTC](https://discourse.itk.org/t/mip/4521 "2021-10-25T21:29:46Z")

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Hi I am trying to generate MIP for 3d brain mra images for aneurysm detection however I am struggling with which libraries to use and how to achieve this with python code

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## [Is there a skull stripping module in SimpleITK that can work with MultiVolume?](https://discourse.itk.org/t/is-there-a-skull-stripping-module-in-simpleitk-that-can-work-with-multivolume/4519)

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**Author:** [@kliron](https://discourse.itk.org/u/kliron)\
**Replies:** 2\
**Last updated:** [October 24, 2021, 6:14am UTC](https://discourse.itk.org/t/is-there-a-skull-stripping-module-in-simpleitk-that-can-work-with-multivolume/4519 "2021-10-24T06:14:47Z")

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I need to do brain extraction from a number of MRI time series (DSC perfusion data). I found this itk module which, unless I am missing something doesn’t seem to support 4D sequences. I can load my DICOM files as a tim…

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## [BinaryErodeImageFilter erodes the entire foreground](https://discourse.itk.org/t/binaryerodeimagefilter-erodes-the-entire-foreground/4518)

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**Author:** [@kliron](https://discourse.itk.org/u/kliron)\
**Replies:** 4\
**Last updated:** [October 22, 2021, 4:15am UTC](https://discourse.itk.org/t/binaryerodeimagefilter-erodes-the-entire-foreground/4518 "2021-10-22T04:15:26Z")

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I have a 3D labelmap image with the values 1 for foreground and 0 for background. I want to erode 1-2 voxels from the edge of the foreground. This is my code: f = sitk.BinaryErodeImageFilter() f.SetKernelType(sitk.sitk…

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## [How to read DICOM's from the Orthanc server?](https://discourse.itk.org/t/how-to-read-dicoms-from-the-orthanc-server/4345)

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**Author:** [@priyanka](https://discourse.itk.org/u/priyanka)\
**Replies:** 7\
**Last updated:** [October 21, 2021, 8:42am UTC](https://discourse.itk.org/t/how-to-read-dicoms-from-the-orthanc-server/4345 "2021-10-21T08:42:06Z")

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DICOM’s are uploaded in orthanc server. I need to take the DICOM’s from the server as a source object in itk.

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