# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=18

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

**Page:** 19

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## [Encountering undefined Behavior when writing DICOM images](https://discourse.itk.org/t/encountering-undefined-behavior-when-writing-dicom-images/4587)

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**Author:** [@Keyn34](https://discourse.itk.org/u/Keyn34)\
**Replies:** 4\
**Last updated:** [November 17, 2021, 3:26pm UTC](https://discourse.itk.org/t/encountering-undefined-behavior-when-writing-dicom-images/4587 "2021-11-17T15:26:05Z")

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Hello everyone, I am currently encountering undefined behavior when trying to write a DICOM series with headers taken from another series. I use only the gdcmIO and loop through all files to read the header with ReadIma…

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## [How to change the radius of the label (.tre file) in TubeTK](https://discourse.itk.org/t/how-to-change-the-radius-of-the-label-tre-file-in-tubetk/4590)

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**Author:** [@noteless](https://discourse.itk.org/u/noteless)\
**Replies:** 3\
**Last updated:** [November 17, 2021, 8:27pm UTC](https://discourse.itk.org/t/how-to-change-the-radius-of-the-label-tre-file-in-tubetk/4590 "2021-11-17T20:27:51Z")

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Using the TubeTK example: ‘Demo-ConvertTubesToImage.ipynb’ and the dataset of ‘100 Healthy Normal MRIs and MRAs from UNC’’ (https://data.kitware.com/#collection/591086ee8d777f16d01e0724/folder/58a372e38d777f0721a64dc6). …

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## [How can I generate and save volume rendered images of brain arteries](https://discourse.itk.org/t/how-can-i-generate-and-save-volume-rendered-images-of-brain-arteries/4575)

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**Author:** [@Aleena\_Suhail](https://discourse.itk.org/u/Aleena_Suhail)\
**Replies:** 9\
**Last updated:** [November 16, 2021, 2:04pm UTC](https://discourse.itk.org/t/how-can-i-generate-and-save-volume-rendered-images-of-brain-arteries/4575 "2021-11-16T14:04:18Z")

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how can I generate and save images that are in nii (nifti) format into volume rendered image using simpleITK

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## [Is there a format for label information (names, color, etc.)](https://discourse.itk.org/t/is-there-a-format-for-label-information-names-color-etc/4579)

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**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 2\
**Last updated:** [November 14, 2021, 10:43pm UTC](https://discourse.itk.org/t/is-there-a-format-for-label-information-names-color-etc/4579 "2021-11-14T22:43:04Z")

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Hi there Is there any convention for storing label information (tissue name, color, index, maybe other metadata) in medical image segmentation? Does ITK support loading/saving this metadata? How does the ML community h…

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## [itk-js: Create Image from Buffer](https://discourse.itk.org/t/itk-js-create-image-from-buffer/2847)

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**Author:** [@Athius](https://discourse.itk.org/u/Athius)\
**Replies:** 5\
**Last updated:** [November 12, 2021, 3:05pm UTC](https://discourse.itk.org/t/itk-js-create-image-from-buffer/2847 "2021-11-12T15:05:44Z")

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Hi everyone, I have some application that transfert a json file that contains buffer of pixels, image dimension, spacing, origin and type of each pixels (int, unsigned int, etc…). I can’t use a standard format like nrrd…

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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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## [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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## [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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## [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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## [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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## [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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## [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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## [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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## [Is it possible to turn on the comments from the SimpleITK youtube channel?](https://discourse.itk.org/t/is-it-possible-to-turn-on-the-comments-from-the-simpleitk-youtube-channel/4505)

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**Author:** [@kolibril13](https://discourse.itk.org/u/kolibril13)\
**Replies:** 2\
**Last updated:** [October 15, 2021, 9:07pm UTC](https://discourse.itk.org/t/is-it-possible-to-turn-on-the-comments-from-the-simpleitk-youtube-channel/4505 "2021-10-15T21:07:40Z")

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I just started to watch the ITK YouTube Tutorials: It would be great if one could make comments there, so that learners can interact with each other.

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## [How to fix Assertion failed: slope == (int)slope with GDCM ImageIO while writing images with double/float slope](https://discourse.itk.org/t/how-to-fix-assertion-failed-slope-int-slope-with-gdcm-imageio-while-writing-images-with-double-float-slope/4487)

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**Author:** [@Keyn34](https://discourse.itk.org/u/Keyn34)\
**Replies:** 1\
**Last updated:** [October 11, 2021, 7:50pm UTC](https://discourse.itk.org/t/how-to-fix-assertion-failed-slope-int-slope-with-gdcm-imageio-while-writing-images-with-double-float-slope/4487 "2021-10-11T19:50:59Z")

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Hello everyone, In advance, I hope this question is okay, as it seems to concern GDCM more than ITK itself. I want to write a 4D series of DICOM images with header data retrieved from another series, basically patching…

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## [About varian obi reconstruction](https://discourse.itk.org/t/about-varian-obi-reconstruction/4483)

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**Author:** [@shun-otsuka](https://discourse.itk.org/u/shun-otsuka)\
**Replies:** 3\
**Last updated:** [October 11, 2021, 5:04pm UTC](https://discourse.itk.org/t/about-varian-obi-reconstruction/4483 "2021-10-11T17:04:55Z")

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Hi, I was trying to reconstruction on Python. I referred to rtk firstreconstraction.py, but it didn’t run well. Can python run the same thing that is run in /RTK/Examples/VarianReconstruction? Please let me know if t…

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## [Convert from 3D numpy array to simple ITK](https://discourse.itk.org/t/convert-from-3d-numpy-array-to-simple-itk/4468)

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**Author:** [@Moha\_data](https://discourse.itk.org/u/Moha_data)\
**Replies:** 3\
**Last updated:** [October 6, 2021, 11:43pm UTC](https://discourse.itk.org/t/convert-from-3d-numpy-array-to-simple-itk/4468 "2021-10-06T23:43:05Z")

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Hello, I have a NumPy array (image\_array) with the size of 400 \* 100 \* 800 (spacing: \[1, 4, 0.1\]). I used the below code to convert it to sitk image for registration: image = sitk.GetImageFromArray(image\_array) image.…

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## [Understanding CompositeTransform discrepancies](https://discourse.itk.org/t/understanding-compositetransform-discrepancies/4474)

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**Author:** [@Theoretialperson](https://discourse.itk.org/u/Theoretialperson)\
**Replies:** 1\
**Last updated:** [October 5, 2021, 6:25pm UTC](https://discourse.itk.org/t/understanding-compositetransform-discrepancies/4474 "2021-10-05T18:25:43Z")

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I’m getting different output from the two code blocks below. The only difference is that in the second I wrap the rotation with a CompositeTransform. I would expect that this transform would just apply the rotation, but …

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## [Getting error while building ITK with cmake](https://discourse.itk.org/t/getting-error-while-building-itk-with-cmake/3173)

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**Author:** [@Usman\_Saeed](https://discourse.itk.org/u/Usman_Saeed)\
**Replies:** 7\
**Last updated:** [October 5, 2021, 4:21pm UTC](https://discourse.itk.org/t/getting-error-while-building-itk-with-cmake/3173 "2021-10-05T16:21:29Z")

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## [Hello World from ITK/Examples/Installation/ not compiling for ITK 5.3](https://discourse.itk.org/t/hello-world-from-itk-examples-installation-not-compiling-for-itk-5-3/4441)

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**Author:** [@krm15](https://discourse.itk.org/u/krm15)\
**Replies:** 11\
**Last updated:** [October 3, 2021, 3:02pm UTC](https://discourse.itk.org/t/hello-world-from-itk-examples-installation-not-compiling-for-itk-5-3/4441 "2021-10-03T15:02:47Z")

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Here is the error message that was popping up on my Mac OSX Big Sur (Apple clang version 12.0.5 (clang-1205.0.22.11)). I fixed it by changing the CMakeLists.txt file. Wanted to post here incase other beginners face the …

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## [Merging Multiple Segmentations into a single LabelMap](https://discourse.itk.org/t/merging-multiple-segmentations-into-a-single-labelmap/4459)

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**Author:** [@msrepo](https://discourse.itk.org/u/msrepo)\
**Replies:** 4\
**Last updated:** [October 1, 2021, 8:14am UTC](https://discourse.itk.org/t/merging-multiple-segmentations-into-a-single-labelmap/4459 "2021-10-01T08:14:19Z")

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Given multiple segmentations from various annotations in different image files, I would like to obtain contour overlays from each segmentations onto the image. Although, I can overlay a single labelmap onto the image li…

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## [Building ITK with python wrappers](https://discourse.itk.org/t/building-itk-with-python-wrappers/4396)

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**Author:** [@Gabriele\_Belotti](https://discourse.itk.org/u/Gabriele_Belotti)\
**Replies:** 10\
**Last updated:** [October 1, 2021, 8:00am UTC](https://discourse.itk.org/t/building-itk-with-python-wrappers/4396 "2021-10-01T08:00:42Z")

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Hi, I was trying to configure ITK (latest master) with CMake with option ITK\_WRAP\_PYTHON on but it keeps failing due to this error: CMake Error at CMake/ITKModuleTest.cmake:196 (message): D:/lib/pyITK\_build/CMakeTmp/…

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## [Computing 95% Hausdorff Distance](https://discourse.itk.org/t/computing-95-hausdorff-distance/3832)

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**Author:** [@emckenzi123](https://discourse.itk.org/u/emckenzi123)\
**Replies:** 6\
**Last updated:** [September 29, 2021, 4:55pm UTC](https://discourse.itk.org/t/computing-95-hausdorff-distance/3832 "2021-09-29T16:55:54Z")

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Hello, I am using Python and SimpleITK, and I would like to access the raw distance values which are used in the calculation of the Hausdorff Distance in order to calculate the 95% Hausdorff Distance. When I use sitk.H…

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## [Detecting multiplanar scout](https://discourse.itk.org/t/detecting-multiplanar-scout/4456)

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**Author:** [@ehh](https://discourse.itk.org/u/ehh)\
**Replies:** 2\
**Last updated:** [September 29, 2021, 12:05pm UTC](https://discourse.itk.org/t/detecting-multiplanar-scout/4456 "2021-09-29T12:05:07Z")

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Hello, I’ve been using itk::ImageSeriesReader to read various DICOM studies, and code similar to that described in the “Process a 2D Slice of a 3D Image” example to extract any of the slices in a series. My code works f…

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