# Uncategorized

**URL:** https://discourse.itk.org/c/uncategorized/1.md?no_subcategories=false&page=6

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

**Page:** 7

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## [DRR](https://discourse.itk.org/t/drr/4637)

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**Author:** [@wangjun456](https://discourse.itk.org/u/wangjun456)\
**Replies:** 0\
**Last updated:** [December 4, 2021, 10:04am UTC](https://discourse.itk.org/t/drr/4637 "2021-12-04T10:04:51Z")

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I use the example GetDRRSiddonJacobsRayTracing.cxx to generate DRR images. The data in the example can generate DRR images. If I change my own data, I can only generate an all black image. Does anyone know why?

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## [2d-3d registration](https://discourse.itk.org/t/2d-3d-registration/4633)

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**Author:** [@wangjun456](https://discourse.itk.org/u/wangjun456)\
**Replies:** 2\
**Last updated:** [December 3, 2021, 1:39am UTC](https://discourse.itk.org/t/2d-3d-registration/4633 "2021-12-03T01:39:39Z")

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Do DSA images need to be converted into X-ray images when cta-dsa cerebrovascular 2D-3D registration?

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## [How to establish type of study](https://discourse.itk.org/t/how-to-establish-type-of-study/4624)

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**Author:** [@Jakub\_Mitura](https://discourse.itk.org/u/Jakub_Mitura)\
**Replies:** 4\
**Last updated:** [December 1, 2021, 2:25pm UTC](https://discourse.itk.org/t/how-to-establish-type-of-study/4624 "2021-12-01T14:25:16Z")

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Hello is it possible given arbitrary dicom files to establish is it computer tomography, pet or MRI using simple itk python library Thanks for help !!

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## [Is it possible to apply a fraction of the transformation that obtained from the registration ?! (Elastix, and Transform)](https://discourse.itk.org/t/is-it-possible-to-apply-a-fraction-of-the-transformation-that-obtained-from-the-registration-elastix-and-transform/4591)

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**Author:** [@Alsurayhi](https://discourse.itk.org/u/Alsurayhi)\
**Replies:** 3\
**Last updated:** [November 18, 2021, 7:25pm UTC](https://discourse.itk.org/t/is-it-possible-to-apply-a-fraction-of-the-transformation-that-obtained-from-the-registration-elastix-and-transform/4591 "2021-11-18T19:25:05Z")

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I have lung CT data. I apply a deformable registration to align the inspiration scan to the expiration scan. I got the registered image and the transformationParamters. I used (transformix -def all) to get the deformati…

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## [How to manipulate DICOM tags on individual slices from python code](https://discourse.itk.org/t/how-to-manipulate-dicom-tags-on-individual-slices-from-python-code/4481)

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**Author:** [@br\_cpvc](https://discourse.itk.org/u/br_cpvc)\
**Replies:** 10\
**Last updated:** [November 17, 2021, 12:38pm UTC](https://discourse.itk.org/t/how-to-manipulate-dicom-tags-on-individual-slices-from-python-code/4481 "2021-11-17T12:38:07Z")

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I use the following code snippet for manipulating DICOM tags on individual slice: ... # insert tags per slice general\_metadata = gdcmIO.GetMetaDataDictionary() metadata\_array = \[\] for slice\_counter in r…

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## [ITK Registrationv4 and PDEDeformableRegistration](https://discourse.itk.org/t/itk-registrationv4-and-pdedeformableregistration/4535)

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**Author:** [@Anurag\_Ranjak](https://discourse.itk.org/u/Anurag_Ranjak)\
**Replies:** 4\
**Last updated:** [November 12, 2021, 3:08pm UTC](https://discourse.itk.org/t/itk-registrationv4-and-pdedeformableregistration/4535 "2021-11-12T15:08:57Z")

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Is it possible to use itk registration v4 algorithms such as SyN or Time Varying Velocity Field transforms in the ITKPython package. I installed the itk package and am doing something like this primary\_image\_path = "fix…

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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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## [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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## [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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## [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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## [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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## [About ImageGraphCut3DSegmentationExample and ImageMultiLabelGraphCut3DSegmentationExample, How to use?](https://discourse.itk.org/t/about-imagegraphcut3dsegmentationexample-and-imagemultilabelgraphcut3dsegmentationexample-how-to-use/4417)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 1\
**Last updated:** [September 22, 2021, 12:43pm UTC](https://discourse.itk.org/t/about-imagegraphcut3dsegmentationexample-and-imagemultilabelgraphcut3dsegmentationexample-how-to-use/4417 "2021-09-22T12:43:16Z")

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I have recently study the " ImageMultiLabelGraphCut3DSegmentationExample", But I did not know how to use the The demo, especially how to make" image.mhd multiLabelMask.mhd backgroundMask.mhd" parameters! Can you give m…

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## [GCC 9/11 Compiler Error or Assembler Error?](https://discourse.itk.org/t/gcc-9-11-compiler-error-or-assembler-error/4412)

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**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 0\
**Last updated:** [September 10, 2021, 10:11pm UTC](https://discourse.itk.org/t/gcc-9-11-compiler-error-or-assembler-error/4412 "2021-09-10T22:11:05Z")

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has anyone seen this error from GCC 9 or 11? FAILED: Plugins/ITKImageProcessing/CMakeFiles/ITKImageProcessingServer.dir/ITKImageProcessingFilters/ITKImageReader.cpp.o $BUILD\_PREFIX/bin/x86\_64-conda-linux-gnu-c++ -DH5Su…

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## [Bug in itk.image\_duplicator?](https://discourse.itk.org/t/bug-in-itk-image-duplicator/4408)

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**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 2\
**Last updated:** [September 9, 2021, 1:56pm UTC](https://discourse.itk.org/t/bug-in-itk-image-duplicator/4408 "2021-09-09T13:56:43Z")

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I load an image like import itk img = itk.imread("/path/to/image.nii.gz") print(type(img)) print(img.shape) The type is a itk.itkImagePython.itkImageF3. The shape is (310,310,310). Then I duplicate the image: img\_t =…

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## [conda-forge release of 5.21?](https://discourse.itk.org/t/conda-forge-release-of-5-21/4402)

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**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 2\
**Last updated:** [September 7, 2021, 3:25pm UTC](https://discourse.itk.org/t/conda-forge-release-of-5-21/4402 "2021-09-07T15:25:01Z")

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I was curious what it takes to track down the errors preventing ITK 5.2.1 from being updated on conda-forge? Thoughts? Mike Jackson

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## [Understanding 3DVersor rotation output](https://discourse.itk.org/t/understanding-3dversor-rotation-output/4389)

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**Author:** [@emilljungberg](https://discourse.itk.org/u/emilljungberg)\
**Replies:** 5\
**Last updated:** [September 4, 2021, 9:44am UTC](https://discourse.itk.org/t/understanding-3dversor-rotation-output/4389 "2021-09-04T09:44:37Z")

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Hi! I’m working on a project where I use a Versor3DRigidTransform for registering 3D MRI images, and I’m having some issues interpreting the output from the registration results. My end goal is to get a transformation w…

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## [control rigidity in bspline registration](https://discourse.itk.org/t/control-rigidity-in-bspline-registration/4380)

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**Author:** [@mary\_na](https://discourse.itk.org/u/mary_na)\
**Replies:** 1\
**Last updated:** [August 29, 2021, 6:47pm UTC](https://discourse.itk.org/t/control-rigidity-in-bspline-registration/4380 "2021-08-29T18:47:21Z")

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Hello! In general the cost function of registration optimization could have two part. One for similarity measurement and the other to control rigidity (registration penalty). In itk I just can change similarity metric. I…

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## [super build simpleitk python wrapping link error](https://discourse.itk.org/t/super-build-simpleitk-python-wrapping-link-error/3126)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 4\
**Last updated:** [June 2, 2020, 1:34pm UTC](https://discourse.itk.org/t/super-build-simpleitk-python-wrapping-link-error/3126 "2020-06-02T13:34:40Z")

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hi all, I have managed to super build simplitk for java, csharp I guess!? but when it gets to swig python wrapping code generation at linking time I get link error because super build has discovered a python37.lib x86 l…

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## [NIfTI-1 or NIfTI-2 Data format](https://discourse.itk.org/t/nifti-1-or-nifti-2-data-format/4330)

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**Author:** [@Iryna\_Galytska](https://discourse.itk.org/u/Iryna_Galytska)\
**Replies:** 4\
**Last updated:** [August 16, 2021, 8:08am UTC](https://discourse.itk.org/t/nifti-1-or-nifti-2-data-format/4330 "2021-08-16T08:08:00Z")

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Could you please advise which data format is used when saving image file e.g. with GetImageFromArray(voxel\_buffer) and ImageFileWriter() NIfTI-1 or NIfTI-2 ? is there posibility to specify explicitly data format (NIfTI-1…

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## [Get anatomical metadata from dicom in Python](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307)

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**Author:** [@banikr](https://discourse.itk.org/u/banikr)\
**Replies:** 13\
**Last updated:** [August 5, 2021, 12:45pm UTC](https://discourse.itk.org/t/get-anatomical-metadata-from-dicom-in-python/4307 "2021-08-05T12:45:52Z")

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I have dicom images converted to nifti format. I need to find if the images are of carotid or coronary vessels from the metadata. I have searched and am convinced that these metadata are not available in Nifti.header. A…

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## [Overlay data Probleam](https://discourse.itk.org/t/overlay-data-probleam/4204)

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**Author:** [@qiangw21](https://discourse.itk.org/u/qiangw21)\
**Replies:** 4\
**Last updated:** [August 5, 2021, 12:04am UTC](https://discourse.itk.org/t/overlay-data-probleam/4204 "2021-08-05T00:04:27Z")

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I can’t read overlay data (6000, 3000). The code below. The result is always “AAAAAAAAAAAAAAAAA…” using ItkPixelType = signed short; constexpr unsigned int Dimension = 2; using ImageType = itk::Image\<ItkPixelT…

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## [What filters would I use to mimic these changes using macOS Preview](https://discourse.itk.org/t/what-filters-would-i-use-to-mimic-these-changes-using-macos-preview/4296)

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**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 1\
**Last updated:** [August 3, 2021, 7:18pm UTC](https://discourse.itk.org/t/what-filters-would-i-use-to-mimic-these-changes-using-macos-preview/4296 "2021-08-03T19:18:43Z")

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I would like to perform the same types of image operations that I performed in macOS Preview.app as shown in the attached image in ITK (specifically in python). Does ITK have filters that would mimic these changes? I…

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## [AttributeError: module 'itk' has no attribute 'AdaptiveHistogramEqualizationImageFilter'](https://discourse.itk.org/t/attributeerror-module-itk-has-no-attribute-adaptivehistogramequalizationimagefilter/4295)

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**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 3\
**Last updated:** [July 30, 2021, 6:47pm UTC](https://discourse.itk.org/t/attributeerror-module-itk-has-no-attribute-adaptivehistogramequalizationimagefilter/4295 "2021-07-30T18:47:52Z")

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I have install through pip ITK 5.2 into an anaconda virtual environment running python 3.8. I am trying to use the AdaptiveHistogramEqualizationImageFilter in my python code and I am getting the following error: Attribu…

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## [Get a leftmost/rightmost coordinate with SimpleITK](https://discourse.itk.org/t/get-a-leftmost-rightmost-coordinate-with-simpleitk/4282)

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**Author:** [@sandyaa013](https://discourse.itk.org/u/sandyaa013)\
**Replies:** 7\
**Last updated:** [July 23, 2021, 3:45pm UTC](https://discourse.itk.org/t/get-a-leftmost-rightmost-coordinate-with-simpleitk/4282 "2021-07-23T15:45:38Z")

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I’m trying to do a project on slicer with simpleITK. I create a labelmap volume node and read it as a SimpleITKimage. Now I show this labelmap volume in red, green and yellow slice window. I want to know how to get a …

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## [Typo in Table 9.2 of ITK manual](https://discourse.itk.org/t/typo-in-table-9-2-of-itk-manual/4280)

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**Author:** [@zhuangming.shen](https://discourse.itk.org/u/zhuangming.shen)\
**Replies:** 1\
**Last updated:** [July 20, 2021, 6:03pm UTC](https://discourse.itk.org/t/typo-in-table-9-2-of-itk-manual/4280 "2021-07-20T18:03:49Z")

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It seems a typo in table 9.2 of ITK manual, Book 1, Updated for ITK version 5.2.0. UL should be SL, which corresponds to signed long.

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## [What's the meaning of slice location (0020, 1041)?](https://discourse.itk.org/t/whats-the-meaning-of-slice-location-0020-1041/4277)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 3\
**Last updated:** [July 19, 2021, 12:10pm UTC](https://discourse.itk.org/t/whats-the-meaning-of-slice-location-0020-1041/4277 "2021-07-19T12:10:07Z")

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I am confuzed abot the slice location (0020, 1041). The explanation (Slice Location Attribute – DICOM Standard Browser) is: Slice Location (0020,1041) is defined as the relative position of the image plane expressed in …

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## [SimpleITK: how to save dicom header into nii.gz file?](https://discourse.itk.org/t/simpleitk-how-to-save-dicom-header-into-nii-gz-file/4278)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 2\
**Last updated:** [July 18, 2021, 1:52pm UTC](https://discourse.itk.org/t/simpleitk-how-to-save-dicom-header-into-nii-gz-file/4278 "2021-07-18T13:52:32Z")

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I can save data into nii.gz file, but I find that the saved file do not include the dicom header information. For example: I load a mha as following: reader = sitk.ImageFileReader() reader.SetFileName("C:\\\\Users\\\\MLoo…

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## [how to speed up the n4 bias correction](https://discourse.itk.org/t/how-to-speed-up-the-n4-bias-correction/4276)

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**Author:** [@asmaharry](https://discourse.itk.org/u/asmaharry)\
**Replies:** 1\
**Last updated:** [July 17, 2021, 10:34pm UTC](https://discourse.itk.org/t/how-to-speed-up-the-n4-bias-correction/4276 "2021-07-17T22:34:15Z")

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I am using SimpleITK bias field correction for my NIFIT images corrector = sitk.N4BiasFieldCorrectionImageFilter() It takes too much time. Is there any way to speed up this process. Thanks.

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## [How to convert DICOM sequence images into a multi frame DICOM file.](https://discourse.itk.org/t/how-to-convert-dicom-sequence-images-into-a-multi-frame-dicom-file/3116)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 9\
**Last updated:** [June 29, 2021, 7:04pm UTC](https://discourse.itk.org/t/how-to-convert-dicom-sequence-images-into-a-multi-frame-dicom-file/3116 "2021-06-29T19:04:35Z")

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Now I have dicom files of one sequence? Totally 117 files. Now I want to write these files into on .dcm File？ How to do it? not use mimics and so on.

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