# Latest

**URL:** https://discourse.itk.org/latest.md?page=59

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

**Page:** 60

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## [help in applying rotation using Affinematrix](https://discourse.itk.org/t/help-in-applying-rotation-using-affinematrix/3592)

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**Author:** [@prms](https://discourse.itk.org/u/prms)\
**Replies:** 1\
**Last updated:** [November 3, 2020, 3:02pm UTC](https://discourse.itk.org/t/help-in-applying-rotation-using-affinematrix/3592 "2020-11-03T15:02:17Z")

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I am using this AffineMatrix to rotate the image by 90 degrees. array(\[\[ 1., 0., 0., 0.\], \[ 0., 0., -1., 0.\], \[ 0., 1., 0., 0.\], \[ 0., 0., 0., 1.\]\]) When I apply this transformation to image(left is the o…

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## [Differentiable Bspline transformation](https://discourse.itk.org/t/differentiable-bspline-transformation/3585)

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**Author:** [@prms](https://discourse.itk.org/u/prms)\
**Replies:** 7\
**Last updated:** [November 4, 2020, 3:05pm UTC](https://discourse.itk.org/t/differentiable-bspline-transformation/3585 "2020-11-04T15:05:49Z")

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I’ve been trying to use B-spline transformation using Neural Networks in PyTorch. I’ve been using the model from here. However, when I use the predicted parameters in SITK, the transformation results do not match. I want…

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## [SimpleITK can not obtain the 0020|000D DICOM tag](https://discourse.itk.org/t/simpleitk-can-not-obtain-the-0020-000d-dicom-tag/3594)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 2\
**Last updated:** [November 4, 2020, 2:22pm UTC](https://discourse.itk.org/t/simpleitk-can-not-obtain-the-0020-000d-dicom-tag/3594 "2020-11-04T14:22:16Z")

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I want to use SimpleITK to obtain the tag information, and the code is: reader = sitk.ImageFileReader() reader.SetFileName(fileName) reader.LoadPrivateTagsOn() reader.ReadImageInformation() if reade…

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## [Read gifti file written by CAT toolbox](https://discourse.itk.org/t/read-gifti-file-written-by-cat-toolbox/3588)

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**Author:** [@crossmanith](https://discourse.itk.org/u/crossmanith)\
**Replies:** 8\
**Last updated:** [November 3, 2020, 4:42pm UTC](https://discourse.itk.org/t/read-gifti-file-written-by-cat-toolbox/3588 "2020-11-03T16:42:52Z")

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Hi, I’d like to postprocess a gifti file written by the CAT toolbox (matlab). It contains one data array with scalar values, one data array with vertices and a third data array with triangles. itk::MeshFileReader offers…

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## [Image with LAB colorspace](https://discourse.itk.org/t/image-with-lab-colorspace/3593)

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**Author:** [@nm97](https://discourse.itk.org/u/nm97)\
**Replies:** 1\
**Last updated:** [November 3, 2020, 4:02pm UTC](https://discourse.itk.org/t/image-with-lab-colorspace/3593 "2020-11-03T16:02:12Z")

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Hi everyone, Just wanted to know how can I have an image with LAB colorspace as it is done for example RGB. itk::Image\<itk::RGBPixel\<InputDataType\>, Diemnsions\> Thank you. Regards, Hrach

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## [scaling is reducing size of image](https://discourse.itk.org/t/scaling-is-reducing-size-of-image/3591)

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**Author:** [@prms](https://discourse.itk.org/u/prms)\
**Replies:** 2\
**Last updated:** [November 3, 2020, 3:10pm UTC](https://discourse.itk.org/t/scaling-is-reducing-size-of-image/3591 "2020-11-03T15:10:25Z")

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I am using an AffineTransform only with scaling parameters and scaling an image. When the scale factor is set to 2, after resampling the image and comparing with the original one in an external viewer, I see that the sca…

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## [reading segmentation file from Slicer (NRRD) with multiple segments with SimpleITK shows Exception](https://discourse.itk.org/t/reading-segmentation-file-from-slicer-nrrd-with-multiple-segments-with-simpleitk-shows-exception/808)

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**Author:** [@Diego\_C](https://discourse.itk.org/u/Diego_C)\
**Replies:** 31\
**Last updated:** [November 3, 2020, 1:29am UTC](https://discourse.itk.org/t/reading-segmentation-file-from-slicer-nrrd-with-multiple-segments-with-simpleitk-shows-exception/808 "2020-11-03T01:29:03Z")

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Hello! I segmented two prostate lesions in Slicer and saved the segmentation as NRRD. \[image\] I am trying to read this file using SimpleITK but I am getting the following error message: File "/Users/odin/anaconda/lib…

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## [How to create an image(like a line) and fused with 3D dicom images ?](https://discourse.itk.org/t/how-to-create-an-image-like-a-line-and-fused-with-3d-dicom-images/3579)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 4\
**Last updated:** [November 2, 2020, 2:24pm UTC](https://discourse.itk.org/t/how-to-create-an-image-like-a-line-and-fused-with-3d-dicom-images/3579 "2020-11-02T14:24:08Z")

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like the title, In fact, I want to create an image and fused with vtkImageData.

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## [Using ITK Modules with itk.js](https://discourse.itk.org/t/using-itk-modules-with-itk-js/3587)

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**Author:** [@Besler](https://discourse.itk.org/u/Besler)\
**Replies:** 0\
**Last updated:** [November 2, 2020, 4:53am UTC](https://discourse.itk.org/t/using-itk-modules-with-itk-js/3587 "2020-11-02T04:53:55Z")

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I am interested in using itk.js with the ITKIOScanco module. Can anyone point me in the right direction for enabling modules in itk.js? Alternatively, I can copy the source into my itk-js build (I think). Also, absolute…

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## [A tool for Fuzzy connectedness Algorithm tool](https://discourse.itk.org/t/a-tool-for-fuzzy-connectedness-algorithm-tool/3577)

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**Author:** [@Nayra\_Ahmed](https://discourse.itk.org/u/Nayra_Ahmed)\
**Replies:** 0\
**Last updated:** [October 28, 2020, 4:30pm UTC](https://discourse.itk.org/t/a-tool-for-fuzzy-connectedness-algorithm-tool/3577 "2020-10-28T16:30:18Z")

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I want to use fuzzy connectedness algorithm in my project, but I knew that it is patented code now , and has been removed from ITK about 10 years ago. So is there any tool that I can buy to use this algorithm through ?

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## [itkPolyLineParametricPathPython to python list](https://discourse.itk.org/t/itkpolylineparametricpathpython-to-python-list/3578)

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**Author:** [@Lee\_Newberg](https://discourse.itk.org/u/Lee_Newberg)\
**Replies:** 0\
**Last updated:** [October 28, 2020, 7:21pm UTC](https://discourse.itk.org/t/itkpolylineparametricpathpython-to-python-list/3578 "2020-10-28T19:21:26Z")

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How do I convert an itk.itkPolyLineParametricPathPython.itkPolyLineParametricPath2 object (produced by itk.contour\_extractor2\_d\_image\_filter) into a Python list of tuples or something similar?

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## [How to import ITKTwoProjectionRegistration module in python](https://discourse.itk.org/t/how-to-import-itktwoprojectionregistration-module-in-python/3576)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 0\
**Last updated:** [October 28, 2020, 11:22am UTC](https://discourse.itk.org/t/how-to-import-itktwoprojectionregistration-module-in-python/3576 "2020-10-28T11:22:30Z")

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I have successfully installed the ITKTwoProjectionRegistration package and now I want to use SiddonJacobsRayCastInterpolateImageFunction function there. I attempted to use this functionality, but unfortunately it is not…

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## [Can I use self-defined cost function for optimization in SimpleITK?](https://discourse.itk.org/t/can-i-use-self-defined-cost-function-for-optimization-in-simpleitk/3575)

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**Author:** [@dada](https://discourse.itk.org/u/dada)\
**Replies:** 1\
**Last updated:** [October 26, 2020, 4:59pm UTC](https://discourse.itk.org/t/can-i-use-self-defined-cost-function-for-optimization-in-simpleitk/3575 "2020-10-26T16:59:57Z")

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Hello, I am doing B-Spline registration, I use Sum of Squared Differences (SSD) as the cost and found images were deformed too much. I would like to add some regularization in the cost function to constrain image deform…

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## [Get Image Metadata of the whole DICOM series \[SimpleITK\]](https://discourse.itk.org/t/get-image-metadata-of-the-whole-dicom-series-simpleitk/3570)

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**Author:** [@ibro45](https://discourse.itk.org/u/ibro45)\
**Replies:** 7\
**Last updated:** [October 26, 2020, 12:32pm UTC](https://discourse.itk.org/t/get-image-metadata-of-the-whole-dicom-series-simpleitk/3570 "2020-10-26T12:32:07Z")

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Hi! Is there a way to adapt the example at Read Image Meta-Data Dictionary and Print so that it shows image metadata of the whole DICOM series? Specifically, with the above example it is possible to read a single dicom…

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## [Does SimpleITK image read from dicom series reflect the view of a 3D-object (axial, coronal and sagital)?](https://discourse.itk.org/t/does-simpleitk-image-read-from-dicom-series-reflect-the-view-of-a-3d-object-axial-coronal-and-sagital/3569)

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**Author:** [@nguyenhoa93](https://discourse.itk.org/u/nguyenhoa93)\
**Replies:** 3\
**Last updated:** [October 24, 2020, 1:53pm UTC](https://discourse.itk.org/t/does-simpleitk-image-read-from-dicom-series-reflect-the-view-of-a-3d-object-axial-coronal-and-sagital/3569 "2020-10-24T13:53:36Z")

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Hi, I am using SimpleITK to read 3D-CT scans from DICOM folders. My scans can belong to any of 3 views: axial, coronal, and sagittal. I did like this: import SimpleITK as sitk dicom\_names = sitk.ImageSeriesReader().Get…

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## [IO DLLs not found](https://discourse.itk.org/t/io-dlls-not-found/3464)

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**Author:** [@simon.rit](https://discourse.itk.org/u/simon.rit)\
**Replies:** 7\
**Last updated:** [October 23, 2020, 7:39pm UTC](https://discourse.itk.org/t/io-dlls-not-found/3464 "2020-10-23T19:39:04Z")

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I am trying to setup the new CI infrastructure in RTK but the windows “build-test-cxx” fails, see When doing the same compilation locally, it turns out that the IO DLLs (ITKIOGDCM-5.2.dll, ITKIOTIFF-5.2.dll, ITKIOMe…

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## [Failure Case with QuadEdgeMesh and Cuberille](https://discourse.itk.org/t/failure-case-with-quadedgemesh-and-cuberille/3565)

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**Author:** [@DVigneault](https://discourse.itk.org/u/DVigneault)\
**Replies:** 0\
**Last updated:** [October 23, 2020, 12:02am UTC](https://discourse.itk.org/t/failure-case-with-quadedgemesh-and-cuberille/3565 "2020-10-23T00:02:39Z")

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Hello all! I’ve run into a bug in the Cuberille remote module, and have finally gotten it down to an MCE which reproduces the issue. I’ve posted a more detailed description of the problem as a github issue, but wanted …

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## [C++20 Comparison Operators](https://discourse.itk.org/t/c-20-comparison-operators/3506)

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**Author:** [@spinicist](https://discourse.itk.org/u/spinicist)\
**Replies:** 5\
**Last updated:** [October 22, 2020, 6:37pm UTC](https://discourse.itk.org/t/c-20-comparison-operators/3506 "2020-10-22T18:37:36Z")

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Hello, Recently Apple updated their Clang, which now supports more of the C++20 standard. Due to the changes in how the comparison operator work in C++20 (to support the spaceship operator as I understand it), I am now …

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## [ImageSeriesReader speed](https://discourse.itk.org/t/imageseriesreader-speed/3558)

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**Author:** [@jwitos](https://discourse.itk.org/u/jwitos)\
**Replies:** 3\
**Last updated:** [October 22, 2020, 5:55pm UTC](https://discourse.itk.org/t/imageseriesreader-speed/3558 "2020-10-22T17:55:23Z")

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Hi everyone, I’m currently using SimpleITK (2.0) ImageSeriesReader to process several hundred of MR studies. I am using the standard approach with GetGDCMSeriesIDs -\> GetGDCMSeriesFileNames -\> Execute. It is working fin…

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## [\[sitk.ImageFileWriter()\] Unable to read a saved image when moved to a different location](https://discourse.itk.org/t/sitk-imagefilewriter-unable-to-read-a-saved-image-when-moved-to-a-different-location/3560)

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**Author:** [@pmody](https://discourse.itk.org/u/pmody)\
**Replies:** 1\
**Last updated:** [October 22, 2020, 1:31pm UTC](https://discourse.itk.org/t/sitk-imagefilewriter-unable-to-read-a-saved-image-when-moved-to-a-different-location/3560 "2020-10-22T13:31:01Z")

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Hi, I save a file with .mha extension as follows. writer = sitk.ImageFileWriter() writer.SetFileName(filepath) writer.SetUseCompression(compression) writer.Execute(data) Problem I am able to read the file via s…

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## [link error. ld: symbol(s) not found for architecture x86\_64](https://discourse.itk.org/t/link-error-ld-symbol-s-not-found-for-architecture-x86-64/3554)

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**Author:** [@kaiyan\_liu](https://discourse.itk.org/u/kaiyan_liu)\
**Replies:** 5\
**Last updated:** [October 22, 2020, 1:13pm UTC](https://discourse.itk.org/t/link-error-ld-symbol-s-not-found-for-architecture-x86-64/3554 "2020-10-22T13:13:22Z")

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I’m learning the examples provided by ITK(https://itk.org/ITKExamples/src/index.htm) when I’m trying the first example( Convert An itk::Image To vtkImageData)(https://itk.org/ITKExamples/src/Bridge/VtkGlue/ConvertAnitkI…

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## [Issues with CMake and ITK installation](https://discourse.itk.org/t/issues-with-cmake-and-itk-installation/3556)

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**Author:** [@Sebastian\_Quezada](https://discourse.itk.org/u/Sebastian_Quezada)\
**Replies:** 2\
**Last updated:** [October 22, 2020, 6:08am UTC](https://discourse.itk.org/t/issues-with-cmake-and-itk-installation/3556 "2020-10-22T06:08:08Z")

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Hi everyone, I’m sorry if this is too basic level question, but I’m having problems installing ITK. Probably the biggest problem of mine is that I’m unfamiliar with computer language such as compilations and the likes, …

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## [Resample volume to specific voxel spacing - SimpleITK](https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531)

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**Author:** [@Tommaso\_Di\_Noto](https://discourse.itk.org/u/Tommaso_Di_Noto)\
**Replies:** 7\
**Last updated:** [October 20, 2020, 7:22am UTC](https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531 "2020-10-20T07:22:49Z")

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Hi everyone! I have a series of 3D, MR volumes acquired from different scanners. I would like to resample all volumes to their median voxel size \[0.39, 0.39, 0.55\] mm. Moreover, for each volume, I also have a binary mas…

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## [Resampling to Isotropic: Signal Processing Theory](https://discourse.itk.org/t/resampling-to-isotropic-signal-processing-theory/1403)

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**Author:** [@Besler](https://discourse.itk.org/u/Besler)\
**Replies:** 18\
**Last updated:** [October 15, 2020, 10:27pm UTC](https://discourse.itk.org/t/resampling-to-isotropic-signal-processing-theory/1403 "2020-10-15T22:27:02Z")

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Hi ITK Community! Sanity check here about Nyquist-Shannon sampling theorem and resampling images to be isotropic. I have read through the online example \[1\]. I have also read the sinc approximation paper \[2\]. Setup I h…

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## [Offset changes with each registration](https://discourse.itk.org/t/offset-changes-with-each-registration/3398)

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**Author:** [@Yew\_Shu\_Ning](https://discourse.itk.org/u/Yew_Shu_Ning)\
**Replies:** 10\
**Last updated:** [October 15, 2020, 9:20pm UTC](https://discourse.itk.org/t/offset-changes-with-each-registration/3398 "2020-10-15T21:20:20Z")

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Hi! I tried to register two images, using the following code: Registration framework setup. registration\_method = sitk.ImageRegistrationMethod() #Set Interpolator registration\_method.SetInterpolator(sitk.sitkLinear) #…

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## [Crop a 3D volumetric medical image](https://discourse.itk.org/t/crop-a-3d-volumetric-medical-image/3540)

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**Author:** [@DL\_Begin](https://discourse.itk.org/u/DL_Begin)\
**Replies:** 2\
**Last updated:** [October 15, 2020, 1:07pm UTC](https://discourse.itk.org/t/crop-a-3d-volumetric-medical-image/3540 "2020-10-15T13:07:41Z")

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Hello , I have two different modality images . CT and PET whole body. For each of them I want to crop the images in x and y dimension such that the background black pixels are removed. I want to get rid of black space o…

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## [3D model -\> DICOM/nii conversion](https://discourse.itk.org/t/3d-model-dicom-nii-conversion/3536)

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**Author:** [@a10227](https://discourse.itk.org/u/a10227)\
**Replies:** 4\
**Last updated:** [October 15, 2020, 10:14am UTC](https://discourse.itk.org/t/3d-model-dicom-nii-conversion/3536 "2020-10-15T10:14:38Z")

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Good day, I have raw patient images as well as their segmentations as 3D models. I need to convert segmentations to 3D image so that this converted image will be aligned with the patient’s one. Could you please tell me…

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## [Set Minimum Python Version to 3.6](https://discourse.itk.org/t/set-minimum-python-version-to-3-6/3528)

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**Author:** [@hjmjohnson](https://discourse.itk.org/u/hjmjohnson)\
**Replies:** 1\
**Last updated:** [October 14, 2020, 1:39pm UTC](https://discourse.itk.org/t/set-minimum-python-version-to-3-6/3528 "2020-10-14T13:39:35Z")

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ITK Community, There is a need to define the minimum python version that is currently supported for building and deploying ITK. Python 3.5 will reach its " end of life " at the end of September 2020. If there are no…

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## [3D Resampling](https://discourse.itk.org/t/3d-resampling/3522)

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**Author:** [@jwitos](https://discourse.itk.org/u/jwitos)\
**Replies:** 4\
**Last updated:** [October 13, 2020, 8:52pm UTC](https://discourse.itk.org/t/3d-resampling/3522 "2020-10-13T20:52:49Z")

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Hi everyone, I am working with a dataset that contains studies acquired in either axial or sagittal plane. I am loading the images with the ImageSeriesReader. Trying to unify the dataset, I would like to resample them t…

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## [How to process CT images one by one and save these images of one series in memory?](https://discourse.itk.org/t/how-to-process-ct-images-one-by-one-and-save-these-images-of-one-series-in-memory/3489)

<div class="topic-metadata">

**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 12\
**Last updated:** [October 10, 2020, 9:42pm UTC](https://discourse.itk.org/t/how-to-process-ct-images-one-by-one-and-save-these-images-of-one-series-in-memory/3489 "2020-10-10T21:42:42Z")

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I have a series of CT images, now I want to process these images one by one, and save these images processed in memory as a 3D data? Then , I can convert this ITK 3D data to VTK image and visual.

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