# Latest

**URL:** https://discourse.itk.org/latest.md?page=45

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

**Page:** 46

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## [Edit a segmentation programatically in simpleitk](https://discourse.itk.org/t/edit-a-segmentation-programatically-in-simpleitk/4512)

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**Author:** [@kliron](https://discourse.itk.org/u/kliron)\
**Replies:** 6\
**Last updated:** [October 20, 2021, 7:07pm UTC](https://discourse.itk.org/t/edit-a-segmentation-programatically-in-simpleitk/4512 "2021-10-20T19:07:57Z")

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Hello, I’m very new to itk/simpleitk. What I need to do is: Segment a volume in an image A (I do this in 3D Slicer, manually). In simpleitk, apply the segmentation in another image, B (assume A and B are different…

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## [Building a TCL package of ITK](https://discourse.itk.org/t/building-a-tcl-package-of-itk/4508)

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**Author:** [@cbellon](https://discourse.itk.org/u/cbellon)\
**Replies:** 3\
**Last updated:** [October 18, 2021, 9:21pm UTC](https://discourse.itk.org/t/building-a-tcl-package-of-itk/4508 "2021-10-18T21:21:58Z")

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Is it possible to generate a TCL package of ITK using SimpleITK?

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## [Binary erode while preserving cell topology](https://discourse.itk.org/t/binary-erode-while-preserving-cell-topology/4499)

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**Author:** [@joachim](https://discourse.itk.org/u/joachim)\
**Replies:** 4\
**Last updated:** [October 18, 2021, 1:43pm UTC](https://discourse.itk.org/t/binary-erode-while-preserving-cell-topology/4499 "2021-10-18T13:43:14Z")

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In Slicer using the Simple Filters module, I’ve been doing binary thresholding of a CT volume: But I want thinner walls so I thought I could fix this with binary erosion: The problem is that the black cells start…

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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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## [Resample produces blurry results when just cropping](https://discourse.itk.org/t/resample-produces-blurry-results-when-just-cropping/4473)

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**Author:** [@Theoretialperson](https://discourse.itk.org/u/Theoretialperson)\
**Replies:** 8\
**Last updated:** [October 14, 2021, 5:35pm UTC](https://discourse.itk.org/t/resample-produces-blurry-results-when-just-cropping/4473 "2021-10-14T17:35:01Z")

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I found out I was getting slightly blurry results when using Resample just with cropping: import SimpleITK as sitk import matplotlib.pyplot as plt import numpy as np def myshow(img, title=None, margin=0.05, dpi=80): …

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## [Use Simpleitk to reading DICOM series In multiple folders](https://discourse.itk.org/t/use-simpleitk-to-reading-dicom-series-in-multiple-folders/4493)

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**Author:** [@kelly90802](https://discourse.itk.org/u/kelly90802)\
**Replies:** 1\
**Last updated:** [October 13, 2021, 12:47pm UTC](https://discourse.itk.org/t/use-simpleitk-to-reading-dicom-series-in-multiple-folders/4493 "2021-10-13T12:47:12Z")

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Hi all, Maybe someone here would know- I want to get the series IDs of each patient. the sitk.ImageSeriesReader.GetGDCMSeriesIDs need all dicom files are included in the file\_path. But, what if the folder structure is…

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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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## [Extraction and fusion of connected domains](https://discourse.itk.org/t/extraction-and-fusion-of-connected-domains/4484)

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**Author:** [@buyierfei](https://discourse.itk.org/u/buyierfei)\
**Replies:** 1\
**Last updated:** [October 8, 2021, 12:57pm UTC](https://discourse.itk.org/t/extraction-and-fusion-of-connected-domains/4484 "2021-10-08T12:57:55Z")

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After analyzing the connected domain of a 3D volume data, several labeled connected domains are obtained. How to obtain the volume data of the corresponding connected domain through the label? What should I do if I want …

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## [After Resampling Process Applying Bias Field Correction](https://discourse.itk.org/t/after-resampling-process-applying-bias-field-correction/4479)

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**Author:** [@Furkan\_Gokhan](https://discourse.itk.org/u/Furkan_Gokhan)\
**Replies:** 2\
**Last updated:** [October 7, 2021, 11:17am UTC](https://discourse.itk.org/t/after-resampling-process-applying-bias-field-correction/4479 "2021-10-07T11:17:05Z")

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Hello everyone, I am using SimpleITK library for bias field correction algorithm to preprocess on MR images but this is very time consuming because MR image ussualy has high dimension such as 152,640,640 pixel array. …

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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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## [Cannot open include file: ‘itkImageIOFactoryRegisterManager.h’ Error in using Conan-built ITK on windows](https://discourse.itk.org/t/cannot-open-include-file-itkimageiofactoryregistermanager-h-error-in-using-conan-built-itk-on-windows/4477)

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**Author:** [@Richard\_Yang](https://discourse.itk.org/u/Richard_Yang)\
**Replies:** 1\
**Last updated:** [October 6, 2021, 1:42pm UTC](https://discourse.itk.org/t/cannot-open-include-file-itkimageiofactoryregistermanager-h-error-in-using-conan-built-itk-on-windows/4477 "2021-10-06T13:42:28Z")

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Hi All, I have encountered an issue as below. |Error|C1083|Cannot open include file: ‘itkImageIOFactoryRegisterManager.h’: No such file or directory|RestDICOM| C:.conan\\5d4232\\1\\include\\ITK-5.1\\itkImageFileWriter.h|246…

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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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## [Image conversion from 3D volume to 2D slices](https://discourse.itk.org/t/image-conversion-from-3d-volume-to-2d-slices/1857)

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**Author:** [@srbn.ghosh89](https://discourse.itk.org/u/srbn.ghosh89)\
**Replies:** 6\
**Last updated:** [October 2, 2021, 11:49am UTC](https://discourse.itk.org/t/image-conversion-from-3d-volume-to-2d-slices/1857 "2021-10-02T11:49:33Z")

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I am finding difficulty to convert a 3D nifti image to slices. Here is a screenshot of input 3D image. And the slices should look like this. But using this code I am getting this type of output slice. The code …

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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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## [Production release of NCI Imaging Data Commons](https://discourse.itk.org/t/production-release-of-nci-imaging-data-commons/4463)

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**Author:** [@fedorov](https://discourse.itk.org/u/fedorov)\
**Replies:** 1\
**Last updated:** [September 29, 2021, 7:13pm UTC](https://discourse.itk.org/t/production-release-of-nci-imaging-data-commons/4463 "2021-09-29T19:13:38Z")

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NCI Imaging Data Commons team is happy to announce the production release of the platform! The main highlights of the production release: the amount of data available increased from ~1TB in the initial pilot release t…

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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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## [Large / slow tests, forbidding parallel execution?](https://discourse.itk.org/t/large-slow-tests-forbidding-parallel-execution/4332)

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**Author:** [@seanm](https://discourse.itk.org/u/seanm)\
**Replies:** 5\
**Last updated:** [September 28, 2021, 6:36pm UTC](https://discourse.itk.org/t/large-slow-tests-forbidding-parallel-execution/4332 "2021-09-28T18:36:20Z")

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Hi all, I recall there is a mechanism to mark ITK tests that shouldn’t run in parallel, but I don’t recall and can’t find what it is. I’m looking to solve some of the timeouts here: https://open.cdash.org/viewTest.php…

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## [How to associate Patient, Study, Series in DICOM file information in C++ itk programming?](https://discourse.itk.org/t/how-to-associate-patient-study-series-in-dicom-file-information-in-c-itk-programming/4452)

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**Author:** [@OrangeJuice3211](https://discourse.itk.org/u/OrangeJuice3211)\
**Replies:** 4\
**Last updated:** [September 28, 2021, 1:05am UTC](https://discourse.itk.org/t/how-to-associate-patient-study-series-in-dicom-file-information-in-c-itk-programming/4452 "2021-09-28T01:05:23Z")

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Hello， I need to read in all Dicom files under the path that I input to get the relationship between Patient, Study and Series. But I can only get all the Tag information by reading a single DCIOM or reading DICOM serie…

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## [How to read series of Dicom images into Django using ITK.js for web volume rendering using VTK.js?](https://discourse.itk.org/t/how-to-read-series-of-dicom-images-into-django-using-itk-js-for-web-volume-rendering-using-vtk-js/4420)

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**Author:** [@Yuvi-416](https://discourse.itk.org/u/Yuvi-416)\
**Replies:** 4\
**Last updated:** [September 27, 2021, 3:28pm UTC](https://discourse.itk.org/t/how-to-read-series-of-dicom-images-into-django-using-itk-js-for-web-volume-rendering-using-vtk-js/4420 "2021-09-27T15:28:24Z")

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Hello everyone, I want to load series of DICOM images into the server and want to visualize it as a volume rendering using vtk.js on the web. As I found here (https://discourse.vtk.org/t/request-hundreds-images-by-http/…

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## [connected components use the same label for different objects](https://discourse.itk.org/t/connected-components-use-the-same-label-for-different-objects/1660)

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**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 3\
**Last updated:** [September 27, 2021, 3:17pm UTC](https://discourse.itk.org/t/connected-components-use-the-same-label-for-different-objects/1660 "2021-09-27T15:17:30Z")

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Dear all, I am writing becaue i am using this method because i want every different object (not connected) with a different value but i obtained but results and i figured out that there are separate objects labeled with…

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## [How to color the segmentation results？](https://discourse.itk.org/t/how-to-color-the-segmentation-results/4454)

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**Author:** [@buyierfei](https://discourse.itk.org/u/buyierfei)\
**Replies:** 1\
**Last updated:** [September 27, 2021, 1:15pm UTC](https://discourse.itk.org/t/how-to-color-the-segmentation-results/4454 "2021-09-27T13:15:51Z")

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When the segmentation results are obtained, how to mark the different segmented areas with different colors, like the fish in the picture, how this is probably achieved

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## [How to obtain the Hu value of DICOM in ITK in C++ programming](https://discourse.itk.org/t/how-to-obtain-the-hu-value-of-dicom-in-itk-in-c-programming/4449)

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**Author:** [@sunrise](https://discourse.itk.org/u/sunrise)\
**Replies:** 3\
**Last updated:** [September 26, 2021, 11:26am UTC](https://discourse.itk.org/t/how-to-obtain-the-hu-value-of-dicom-in-itk-in-c-programming/4449 "2021-09-26T11:26:23Z")

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I can get the pixel value by converteing DICOM to mat through OpenCVImageBridge, but I would have some trouble when adjusting the window width and window center. I don’t know whether you have a method that we can obtain …

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## [Unresolved symbol when using watershed](https://discourse.itk.org/t/unresolved-symbol-when-using-watershed/4444)

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**Author:** [@xh\_c](https://discourse.itk.org/u/xh_c)\
**Replies:** 4\
**Last updated:** [September 24, 2021, 4:13pm UTC](https://discourse.itk.org/t/unresolved-symbol-when-using-watershed/4444 "2021-09-24T16:13:46Z")

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Hi, I am using itk::WatershedImageFilter in my project and got Unresolved symbol error: I search the Internet and found add ITKAlgorithms in target\_link\_libraries may help. But I got error say ITKAlgorithms.lib not …

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## [Transforming Point not working when flipping](https://discourse.itk.org/t/transforming-point-not-working-when-flipping/4446)

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**Author:** [@kleingeo](https://discourse.itk.org/u/kleingeo)\
**Replies:** 4\
**Last updated:** [September 24, 2021, 12:22pm UTC](https://discourse.itk.org/t/transforming-point-not-working-when-flipping/4446 "2021-09-24T12:22:50Z")

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I am working on a data augmentation pipeline with a translations, rotation, scaling, flipping, and elastic deformation. I need to track how landmarks are modified during the transformation and resampling process, but the…

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## [How could I get the TP, FP, FN, TN?](https://discourse.itk.org/t/how-could-i-get-the-tp-fp-fn-tn/1936)

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**Author:** [@hubutui](https://discourse.itk.org/u/hubutui)\
**Replies:** 3\
**Last updated:** [September 24, 2021, 8:25am UTC](https://discourse.itk.org/t/how-could-i-get-the-tp-fp-fn-tn/1936 "2021-09-24T08:25:14Z")

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I’m trying to evaluate my segmentation result. I could use sitk.LabelOverlapMeasuresImageFilter to get dice, FPR, FNR. I wonder if there any filter for calculating confusion matrix so that I could calcalate every metric …

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