# Latest

**URL:** https://discourse.itk.org/latest.md?page=31

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

**Page:** 32

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## [sitk Commands for N4](https://discourse.itk.org/t/sitk-commands-for-n4/5465)

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**Author:** [@spinicist](https://discourse.itk.org/u/spinicist)\
**Replies:** 7\
**Last updated:** [November 17, 2022, 4:37pm UTC](https://discourse.itk.org/t/sitk-commands-for-n4/5465 "2022-11-17T16:37:19Z")

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Hello, I’d like to add loggin for N4BiasFieldCorrection in sitk, similar to that printed out by the ANTs version. However, it looks like the GetCurrentConvergenceMeasurement and GetCurrentLevel methods are not currentl…

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## ['itk' has no attribute 'structure\_preserving\_color\_normalization\_filter'](https://discourse.itk.org/t/itk-has-no-attribute-structure-preserving-color-normalization-filter/5498)

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**Author:** [@Jon](https://discourse.itk.org/u/Jon)\
**Replies:** 2\
**Last updated:** [November 17, 2022, 11:58am UTC](https://discourse.itk.org/t/itk-has-no-attribute-structure-preserving-color-normalization-filter/5498 "2022-11-17T11:58:22Z")

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The Python 3.8 script below fails with: AttributeError: module ‘itk’ has no attribute ‘structure\_preserving\_color\_normalization\_filter’ # https://www.kitware.com/new-insight-toolkit-itk-module-for-structure-preserving-…

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## [Remove Noisy Objects](https://discourse.itk.org/t/remove-noisy-objects/5492)

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**Author:** [@cristinamontserrat](https://discourse.itk.org/u/cristinamontserrat)\
**Replies:** 1\
**Last updated:** [November 16, 2022, 3:12pm UTC](https://discourse.itk.org/t/remove-noisy-objects/5492 "2022-11-16T15:12:28Z")

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Hi! I am trying to remove labels from Label Map, which belong to noisy objects. For doing that, I have created the following code: ITKImgLabelType2D::Pointer RemoveNoisyObjects( const ITKImgLabelType2D::Pointer& imgIn,…

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## [itk 5.3rc4.post3: Failure to load libtbb library (observed on macOS 10.13)](https://discourse.itk.org/t/itk-5-3rc4-post3-failure-to-load-libtbb-library-observed-on-macos-10-13/5405)

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**Author:** [@jcfr](https://discourse.itk.org/u/jcfr)\
**Replies:** 3\
**Last updated:** [November 14, 2022, 1:55pm UTC](https://discourse.itk.org/t/itk-5-3rc4-post3-failure-to-load-libtbb-library-observed-on-macos-10-13/5405 "2022-11-14T13:55:47Z")

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To follow up on ITK 5.3 Release Candidate 4 available for testing, I may have identified few issues found with itk 5.3rc4.post3 specific to macOS that are related to the bundling of libtbb.12.3.dylib. Context While the …

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## [Linking itk with an external project](https://discourse.itk.org/t/linking-itk-with-an-external-project/5481)

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**Author:** [@Ajay\_Emmanuel](https://discourse.itk.org/u/Ajay_Emmanuel)\
**Replies:** 5\
**Last updated:** [November 11, 2022, 7:59pm UTC](https://discourse.itk.org/t/linking-itk-with-an-external-project/5481 "2022-11-11T19:59:16Z")

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Hi, I built the latest version of itk using CMake. After configuring my CMakeLists.txt file in as per the instructions online for an external project, I am still getting this error - cannot open source file “itkImage.h”…

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## [How can I keep the association between input image coordinate (z-axis) and segmentation mask?](https://discourse.itk.org/t/how-can-i-keep-the-association-between-input-image-coordinate-z-axis-and-segmentation-mask/5467)

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**Author:** [@DushiFdo](https://discourse.itk.org/u/DushiFdo)\
**Replies:** 7\
**Last updated:** [November 11, 2022, 1:46pm UTC](https://discourse.itk.org/t/how-can-i-keep-the-association-between-input-image-coordinate-z-axis-and-segmentation-mask/5467 "2022-11-11T13:46:35Z")

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Hello, I am working with 3D CT images which are consists of a series of 2D slices. I resized them into (128 x 128 x 128) My segmentation masks are provided as xml files and have segmentations only for like 3 or 4 slice…

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## [RuntimeError: Exception thrown in SimpleITK ImageSeriesReader\_Execute](https://discourse.itk.org/t/runtimeerror-exception-thrown-in-simpleitk-imageseriesreader-execute/5484)

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**Author:** [@DushiFdo](https://discourse.itk.org/u/DushiFdo)\
**Replies:** 0\
**Last updated:** [November 11, 2022, 1:50am UTC](https://discourse.itk.org/t/runtimeerror-exception-thrown-in-simpleitk-imageseriesreader-execute/5484 "2022-11-11T01:50:42Z")

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I am trying to read a 3D dicom image with sitk as follows: def read\_first\_series\_in\_dir(dir): series\_reader = sitk.ImageSeriesReader() series\_IDs = sitk.ImageSeriesReader.GetGDCMSeriesIDs(dir) series\_file\_na…

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## [How to change the order of rotation in SetComputeZYX()?](https://discourse.itk.org/t/how-to-change-the-order-of-rotation-in-setcomputezyx/5474)

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**Author:** [@suzume](https://discourse.itk.org/u/suzume)\
**Replies:** 5\
**Last updated:** [November 11, 2022, 1:08am UTC](https://discourse.itk.org/t/how-to-change-the-order-of-rotation-in-setcomputezyx/5474 "2022-11-11T01:08:03Z")

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I want to generate DRR from a CT image. I want the CT image to rotate in the order of the X, Y, Z axis. However, SetComputeZYX( ) only set the order ZYX/ZXY. How can I can set the order XYZ?

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## [What type of transformation aligns the centres of the two volumes?](https://discourse.itk.org/t/what-type-of-transformation-aligns-the-centres-of-the-two-volumes/5470)

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**Author:** [@mahesh\_bhosale](https://discourse.itk.org/u/mahesh_bhosale)\
**Replies:** 4\
**Last updated:** [November 8, 2022, 11:15pm UTC](https://discourse.itk.org/t/what-type-of-transformation-aligns-the-centres-of-the-two-volumes/5470 "2022-11-08T23:15:48Z")

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I am working on the medical image registration task which requires two volumes to be affinely aligned globally, what transformation should I apply to make them aligned?

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## [ITK 5.3 Release Candidate 2 available for testing](https://discourse.itk.org/t/itk-5-3-release-candidate-2-available-for-testing/4573)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 6\
**Last updated:** [November 7, 2022, 5:02pm UTC](https://discourse.itk.org/t/itk-5-3-release-candidate-2-available-for-testing/4573 "2022-11-07T17:02:45Z")

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ITK 5.3 Release Candidate 2 Release Notes We are happy to announce the Insight Toolkit (ITK) 5.3 Release Candidate 2 is available for testing! :tada: ITK is an open-source, cross-platform toolkit for N-dimensional scient…

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## [How can I apply a 2D mask in a 3D image? - SliceBySliceImageFilter](https://discourse.itk.org/t/how-can-i-apply-a-2d-mask-in-a-3d-image-slicebysliceimagefilter/5418)

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**Author:** [@cristinamontserrat](https://discourse.itk.org/u/cristinamontserrat)\
**Replies:** 11\
**Last updated:** [November 7, 2022, 8:56am UTC](https://discourse.itk.org/t/how-can-i-apply-a-2d-mask-in-a-3d-image-slicebysliceimagefilter/5418 "2022-11-07T08:56:24Z")

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Hi! I am trying to mask a 3D image with a 2D mask with the itkSliceBySliceImageFilter. Here is my code: // We create the filter mask using MaskFilterType = itk::MaskImageFilter\<ITKImgLabelType2D, ITKImgLabelType2D, I…

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## [measure lesion size](https://discourse.itk.org/t/measure-lesion-size/5469)

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**Author:** [@Jakub\_Mitura1](https://discourse.itk.org/u/Jakub_Mitura1)\
**Replies:** 2\
**Last updated:** [November 6, 2022, 6:11am UTC](https://discourse.itk.org/t/measure-lesion-size/5469 "2022-11-06T06:11:04Z")

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Hello I have a lesion in the 3d boolean array - 1 is presence 0 is absence - I would like to get the size of it in 3 axes - main longest axis and the other 2. Problem is that the long axis of the lesion generally do not…

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## [After switching to python 3.10 I can no longer pip install the same versions of itk as when using python 3.9.](https://discourse.itk.org/t/after-switching-to-python-3-10-i-can-no-longer-pip-install-the-same-versions-of-itk-as-when-using-python-3-9/5466)

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**Author:** [@br\_cpvc](https://discourse.itk.org/u/br_cpvc)\
**Replies:** 5\
**Last updated:** [November 4, 2022, 12:48pm UTC](https://discourse.itk.org/t/after-switching-to-python-3-10-i-can-no-longer-pip-install-the-same-versions-of-itk-as-when-using-python-3-9/5466 "2022-11-04T12:48:07Z")

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I’m not entirely sure if this is the expected behavior or not. I have tried to find the root cause of this, but I lack the knowledge of how the internals work and I’m not able to find the cause. As far as I can see https…

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## [How can I read/write series of .tiff in webpage using itk.js?](https://discourse.itk.org/t/how-can-i-read-write-series-of-tiff-in-webpage-using-itk-js/5464)

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**Author:** [@Yuvi-416](https://discourse.itk.org/u/Yuvi-416)\
**Replies:** 2\
**Last updated:** [November 4, 2022, 12:00pm UTC](https://discourse.itk.org/t/how-can-i-read-write-series-of-tiff-in-webpage-using-itk-js/5464 "2022-11-04T12:00:55Z")

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Hi all, I am trying to read a series of .tiff or .tif files into the webpage using ITK.js. I know it supports it as it’s here Supported Image File Formats | itk-wasm and it says I have to use the readImageFileSeries fun…

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## [How to output label map in C++?](https://discourse.itk.org/t/how-to-output-label-map-in-c/5459)

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**Author:** [@SummerZ2020](https://discourse.itk.org/u/SummerZ2020)\
**Replies:** 5\
**Last updated:** [November 4, 2022, 12:55am UTC](https://discourse.itk.org/t/how-to-output-label-map-in-c/5459 "2022-11-04T00:55:47Z")

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hello, I am using label map to remove some undesirable regions in binary image. first, call BinaryImageToShapeLabelMapFilter to get label map, then output the label map and all the objects’ centroids. I have checked t…

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## [ThreadFunctionType, ITK\_THREAD\_RETURN\_TYPE, and 32-bit Windows](https://discourse.itk.org/t/threadfunctiontype-itk-thread-return-type-and-32-bit-windows/5457)

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**Author:** [@gcsharp](https://discourse.itk.org/u/gcsharp)\
**Replies:** 3\
**Last updated:** [November 2, 2022, 7:56pm UTC](https://discourse.itk.org/t/threadfunctiontype-itk-thread-return-type-and-32-bit-windows/5457 "2022-11-02T19:56:39Z")

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Hi, I encountered a problem on 32-bit windows for ITK 5.X. In ITK 4, thread functions were defined as follows: typedef unsigned(\_\_stdcall \* ThreadFunctionType)(void \*); #define ITK\_THREAD\_RETURN\_TYPE unsigned \_\_stdcall…

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## [Label Shape Opening Slice by Slice not working very welll](https://discourse.itk.org/t/label-shape-opening-slice-by-slice-not-working-very-welll/5454)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 0\
**Last updated:** [October 27, 2022, 8:12pm UTC](https://discourse.itk.org/t/label-shape-opening-slice-by-slice-not-working-very-welll/5454 "2022-10-27T20:12:56Z")

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Can’t apply shape open slice by slice. I get a null image, even though most of the connected components have less than 1000 pixels… for(int slice\_to\_process = 0; slice\_to\_process \< final\_slice\_ribs ; slice\_to\_process++)…

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## [Rotated an Image but can't get an object count](https://discourse.itk.org/t/rotated-an-image-but-cant-get-an-object-count/5453)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 1\
**Last updated:** [October 27, 2022, 6:57pm UTC](https://discourse.itk.org/t/rotated-an-image-but-cant-get-an-object-count/5453 "2022-10-27T18:57:25Z")

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I rotated an image with euler3d transform and resampler and it works fine. But then I ask to get an object count and get 0 objects which is not true based on the saved image. using ResampleFilterType\_2 = itk::ResampleIm…

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## [Processing two images with different starts](https://discourse.itk.org/t/processing-two-images-with-different-starts/5451)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 1\
**Last updated:** [October 27, 2022, 1:15pm UTC](https://discourse.itk.org/t/processing-two-images-with-different-starts/5451 "2022-10-27T13:15:04Z")

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I have 2 images with the same size but with different starts. I want use one as a mask. Should I use import image filter first to set the same start for both of them?

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## [Adding additional geometries to Viewer changes colours of outputs](https://discourse.itk.org/t/adding-additional-geometries-to-viewer-changes-colours-of-outputs/5449)

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**Author:** [@Kevin\_Sweeney](https://discourse.itk.org/u/Kevin_Sweeney)\
**Replies:** 3\
**Last updated:** [October 26, 2022, 1:30pm UTC](https://discourse.itk.org/t/adding-additional-geometries-to-viewer-changes-colours-of-outputs/5449 "2022-10-26T13:30:18Z")

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I am visualising multiple outputs in the same view depending on choices by the user (i.e. highlighting points on top of glyphs etc). However, I am finding that as I add additional glyphs the colours of other sources cha…

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## [runPipelineNode](https://discourse.itk.org/t/runpipelinenode/5271)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 3\
**Last updated:** [October 26, 2022, 6:34am UTC](https://discourse.itk.org/t/runpipelinenode/5271 "2022-10-26T06:34:19Z")

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Hi everyone, I have hard time to extend ITK-WASM HelloWasm example to MedianFilterTest.cxx example. I managed to build it using itk-wasm build command in node.js terminal command line in VSCODE. MedianFilterTest.js/umd/…

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## [ITK read multi-frame DCM files](https://discourse.itk.org/t/itk-read-multi-frame-dcm-files/5444)

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**Author:** [@itkk](https://discourse.itk.org/u/itkk)\
**Replies:** 3\
**Last updated:** [October 25, 2022, 4:16pm UTC](https://discourse.itk.org/t/itk-read-multi-frame-dcm-files/5444 "2022-10-25T16:16:17Z")

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Can ITK read multi-frame DCM files? For example, DSA, how to do it?

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## [Each voxel (3-dimmensional pixel) in the image has a length, width, and height of 1mm. What will be the volume in cm^3?](https://discourse.itk.org/t/each-voxel-3-dimmensional-pixel-in-the-image-has-a-length-width-and-height-of-1mm-what-will-be-the-volume-in-cm-3/5438)

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**Author:** [@dharmannasdmit](https://discourse.itk.org/u/dharmannasdmit)\
**Replies:** 1\
**Last updated:** [October 23, 2022, 11:51pm UTC](https://discourse.itk.org/t/each-voxel-3-dimmensional-pixel-in-the-image-has-a-length-width-and-height-of-1mm-what-will-be-the-volume-in-cm-3/5438 "2022-10-23T23:51:57Z")

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dimension of image is 256X256X192 T2\_76.IMA (130.1 KB) Each voxel (3-dimmensional pixel) in this image has a length, width, and height of 1mm. Calculate brain volume from brainMask. What is the volume of this brain in …

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## [DICOM Enhanced CT with GDCM\_IO](https://discourse.itk.org/t/dicom-enhanced-ct-with-gdcm-io/5402)

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**Author:** [@rfrank](https://discourse.itk.org/u/rfrank)\
**Replies:** 7\
**Last updated:** [October 21, 2022, 3:48pm UTC](https://discourse.itk.org/t/dicom-enhanced-ct-with-gdcm-io/5402 "2022-10-21T15:48:40Z")

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Hi I’m working on an existing code base that uses ITK/Gdcm ITK 4.12 I have a Toshiba ct multi frame. ITK is returning direction cosines 1 0 0 0 1 0 0 0 -1 And I need to swap the z axis and reset the direction cosine…

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## [how to implement registration between DSA(2d)-CTA(3d) image](https://discourse.itk.org/t/how-to-implement-registration-between-dsa-2d-cta-3d-image/5415)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 11\
**Last updated:** [October 21, 2022, 1:56am UTC](https://discourse.itk.org/t/how-to-implement-registration-between-dsa-2d-cta-3d-image/5415 "2022-10-21T01:56:12Z")

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Is there any method to register DSA(2d)-CTA(3d) images? For every point in CTA, I want to know the corresponding point in DSA. I find an example for 2d-3d registration. In this ITKTwoProjectionRegistration, I don’t know…

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## [import image axis reorder and flipping](https://discourse.itk.org/t/import-image-axis-reorder-and-flipping/5433)

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**Author:** [@leandro328](https://discourse.itk.org/u/leandro328)\
**Replies:** 2\
**Last updated:** [October 20, 2022, 8:06pm UTC](https://discourse.itk.org/t/import-image-axis-reorder-and-flipping/5433 "2022-10-20T20:06:21Z")

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i need to work with itk images and numpy arrays, but the operations itk.GetImageFromArray and itk.GetArrayFromImage e.g.: img = itk.GetImageFromArray(input\_img) res\_img = itk.GetArrayFromImage(img) are flipping and a…

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## [Ability to show text actor in itkwidgets.view()](https://discourse.itk.org/t/ability-to-show-text-actor-in-itkwidgets-view/5431)

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**Author:** [@Kevin\_Sweeney](https://discourse.itk.org/u/Kevin_Sweeney)\
**Replies:** 0\
**Last updated:** [October 20, 2022, 3:18pm UTC](https://discourse.itk.org/t/ability-to-show-text-actor-in-itkwidgets-view/5431 "2022-10-20T15:18:49Z")

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I am just looking to confirm that it is not possible to add BillboardTextActor3D to viewer geometries. I have tried a few things, but as the warning stipulates: The 'geometries' trait of a Viewer instance expected A dat…

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## [Retrieve info on current itkwidget.view window bounds - following zoom](https://discourse.itk.org/t/retrieve-info-on-current-itkwidget-view-window-bounds-following-zoom/5420)

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**Author:** [@Kevin\_Sweeney](https://discourse.itk.org/u/Kevin_Sweeney)\
**Replies:** 4\
**Last updated:** [October 19, 2022, 6:19pm UTC](https://discourse.itk.org/t/retrieve-info-on-current-itkwidget-view-window-bounds-following-zoom/5420 "2022-10-19T18:19:31Z")

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As point selection in itkwidgets.view is not currently possible (Geometry / Point selection · Issue #575 · Kitware/itk-vtk-viewer · GitHub) is there a way to get the visual bounds of the viewer? i.e. if we create a view …

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## [How accelerate many times affinetransform, fft and ifft process?](https://discourse.itk.org/t/how-accelerate-many-times-affinetransform-fft-and-ifft-process/5425)

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**Author:** [@ydl](https://discourse.itk.org/u/ydl)\
**Replies:** 3\
**Last updated:** [October 19, 2022, 2:22pm UTC](https://discourse.itk.org/t/how-accelerate-many-times-affinetransform-fft-and-ifft-process/5425 "2022-10-19T14:22:08Z")

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I have many mri(ixi-t2 dataset with.nii.gz format), for each image, what I now do is, create n copies of this image(n is select from(30, 150), for each copy, do random affinetransform, then fft to k-space, for this n k-s…

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## [Euler3DTransform class and Transforms class](https://discourse.itk.org/t/euler3dtransform-class-and-transforms-class/5332)

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**Author:** [@natwille1](https://discourse.itk.org/u/natwille1)\
**Replies:** 6\
**Last updated:** [October 19, 2022, 1:21pm UTC](https://discourse.itk.org/t/euler3dtransform-class-and-transforms-class/5332 "2022-10-19T13:21:00Z")

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I executed a ImageRegistrationMethod function call, and set the initial transform according to: initial\_transform = sitk.CenteredTransformInitializer( fixed\_image, moving\_image, sitk.Euler3DTransform(), …

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