# Latest

**URL:** https://discourse.itk.org/latest.md?page=30

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

**Page:** 31

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## [Can't compile ITKElastix with python bindings:](https://discourse.itk.org/t/cant-compile-itkelastix-with-python-bindings/5546)

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**Author:** [@eric](https://discourse.itk.org/u/eric)\
**Replies:** 4\
**Last updated:** [December 8, 2022, 7:22pm UTC](https://discourse.itk.org/t/cant-compile-itkelastix-with-python-bindings/5546 "2022-12-08T19:22:48Z")

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Hi, I started compiling ITKElastix with python bindings but I keep getting errors like these: elxParameterObject: warning(4): ITK type not wrapped, or currently not known: itk::DataObject elxParameterObject: warnin…

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## [Writing DICOM Spacing Between Slices](https://discourse.itk.org/t/writing-dicom-spacing-between-slices/4552)

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**Author:** [@wwwalewww](https://discourse.itk.org/u/wwwalewww)\
**Replies:** 5\
**Last updated:** [December 8, 2022, 2:15pm UTC](https://discourse.itk.org/t/writing-dicom-spacing-between-slices/4552 "2022-12-08T14:15:46Z")

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Hello, I’m trying to write a DICOM series after some image processing, and to do that I’m following the code in the example. Since I upsampled the volume, the spacing between slices has changed and I added it to the ta…

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## [How to use ITK multi threading primitives to do parallel execution of loop iteration](https://discourse.itk.org/t/how-to-use-itk-multi-threading-primitives-to-do-parallel-execution-of-loop-iteration/5531)

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**Author:** [@br\_cpvc](https://discourse.itk.org/u/br_cpvc)\
**Replies:** 6\
**Last updated:** [December 7, 2022, 9:34am UTC](https://discourse.itk.org/t/how-to-use-itk-multi-threading-primitives-to-do-parallel-execution-of-loop-iteration/5531 "2022-12-07T09:34:58Z")

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I am currently working on a patch which accelerates the execution speed of the ANTs Atropos application. I have until now been using openmp to implement the acceleration. The suggested code changes and initial related di…

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## [Pre-processing segmentation mask](https://discourse.itk.org/t/pre-processing-segmentation-mask/5530)

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**Author:** [@DushiFdo](https://discourse.itk.org/u/DushiFdo)\
**Replies:** 9\
**Last updated:** [December 6, 2022, 7:31pm UTC](https://discourse.itk.org/t/pre-processing-segmentation-mask/5530 "2022-12-06T19:31:30Z")

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I am working with 3D CT images (Dicoms), and I performed several pre-processing steps on the input images such as resampling, normalizing, removing noise, crop image, resizing, crop center and reshaping to (128, 128, 128…

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## [Confocal images alignment issues](https://discourse.itk.org/t/confocal-images-alignment-issues/5550)

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**Author:** [@Spiran](https://discourse.itk.org/u/Spiran)\
**Replies:** 3\
**Last updated:** [December 6, 2022, 5:02pm UTC](https://discourse.itk.org/t/confocal-images-alignment-issues/5550 "2022-12-06T17:02:46Z")

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Hello, I am facing a problem with ITK alignment . More specifically, when I upload my images the outpout score before alignment is usually 0,05 to 0,1 after the registration the highest score that I got is 0.7 (after cr…

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## [How to set pre-defined points in the fixed image in gui?](https://discourse.itk.org/t/how-to-set-pre-defined-points-in-the-fixed-image-in-gui/5519)

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**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 5\
**Last updated:** [December 2, 2022, 6:53am UTC](https://discourse.itk.org/t/how-to-set-pre-defined-points-in-the-fixed-image-in-gui/5519 "2022-12-02T06:53:32Z")

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Hello, I have a list of pre-defined co-ordinates written in a text file. I want to mark these co-ordinates in the fixed image in the gui. After the marked fixed image is obtained, the corresponding co-ordinates in t…

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## [Unsupported compiler in Qt](https://discourse.itk.org/t/unsupported-compiler-in-qt/5538)

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**Author:** [@Ellen-D216](https://discourse.itk.org/u/Ellen-D216)\
**Replies:** 1\
**Last updated:** [December 1, 2022, 4:45pm UTC](https://discourse.itk.org/t/unsupported-compiler-in-qt/5538 "2022-12-01T16:45:26Z")

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Hello, I successfully built ITK5.2 libraries with gcc11, but having an issue using ITK in Qt. I’m getting an “Unsupported compiler” error thrown by the generated include file itk\_compiler\_detection.h from this conditio…

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## [2d/3d registration](https://discourse.itk.org/t/2d-3d-registration/5539)

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**Author:** [@zx-lhb](https://discourse.itk.org/u/zx-lhb)\
**Replies:** 0\
**Last updated:** [December 1, 2022, 9:10am UTC](https://discourse.itk.org/t/2d-3d-registration/5539 "2022-12-01T09:10:11Z")

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I have tried to run the 2d/3d registration example tourial in my own CT dataset by defalut parameters setting. and it worked fine, got 6 transformation parameters and output result images. But I don’t actually know what …

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## [2D to 3D Registration](https://discourse.itk.org/t/2d-to-3d-registration/2112)

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**Author:** [@svabhishek29](https://discourse.itk.org/u/svabhishek29)\
**Replies:** 21\
**Last updated:** [December 1, 2022, 5:16am UTC](https://discourse.itk.org/t/2d-to-3d-registration/2112 "2022-12-01T05:16:48Z")

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hi, i was looking an example for registration of 2D images with 3D images, i can’t find any examples on this topic. can someone please direct me to an example or a library that can do this Thanks

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## [2D3D registration](https://discourse.itk.org/t/2d3d-registration/5533)

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**Author:** [@suzume](https://discourse.itk.org/u/suzume)\
**Replies:** 1\
**Last updated:** [November 30, 2022, 3:01pm UTC](https://discourse.itk.org/t/2d3d-registration/5533 "2022-11-30T15:01:38Z")

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Hi, I want to register the 3D CT image with the 2D image. The IntensityBased2D3DRegistration.cxx needs a pair of 2D orthographic images. And I only have one 2D image. Can I treat this 2D image as a 3D image and register …

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## [SimpleITK on alternate HW arches (ppc64le/aarch64)](https://discourse.itk.org/t/simpleitk-on-alternate-hw-arches-ppc64le-aarch64/1812)

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**Author:** [@jayfurmanek](https://discourse.itk.org/u/jayfurmanek)\
**Replies:** 11\
**Last updated:** [November 30, 2022, 6:36am UTC](https://discourse.itk.org/t/simpleitk-on-alternate-hw-arches-ppc64le-aarch64/1812 "2022-11-30T06:36:22Z")

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Hi ITK community! I’ve been running SimpleITK on ppc64le (IBM Power9 systems) and it builds and runs great. I was thinking it would be easier to contribute back for me and my team if there was a Travis job that would bu…

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## [Transformation of Image volumes of different MRI imaging techniques](https://discourse.itk.org/t/transformation-of-image-volumes-of-different-mri-imaging-techniques/5527)

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**Author:** [@c.spanakis83](https://discourse.itk.org/u/c.spanakis83)\
**Replies:** 6\
**Last updated:** [November 30, 2022, 12:01am UTC](https://discourse.itk.org/t/transformation-of-image-volumes-of-different-mri-imaging-techniques/5527 "2022-11-30T00:01:12Z")

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Hello. I want to apply an image registration on two brain MR T1images (say MRT1 A and MRT1 B after the names of the patients A and B). Additionally, A and B have their diffusion MRI brain image which are fully aligned wi…

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## [Segmentation fault when running static linked executable on Ubuntu](https://discourse.itk.org/t/segmentation-fault-when-running-static-linked-executable-on-ubuntu/4826)

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**Author:** [@Keyn34](https://discourse.itk.org/u/Keyn34)\
**Replies:** 1\
**Last updated:** [November 29, 2022, 2:37pm UTC](https://discourse.itk.org/t/segmentation-fault-when-running-static-linked-executable-on-ubuntu/4826 "2022-11-29T14:37:26Z")

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Hey everyone (again :)), I’m trying to run a static linked executable on Ubuntu 20.04.3. For this purpose, I configured ITK 5.2.1 with CMake, made sure to set BUILD\_SHARED\_LIBS and ITK\_DYNAMIC\_LOADING to OFF, and procee…

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## [How to get m\_LineContainer from the labelObject?](https://discourse.itk.org/t/how-to-get-m-linecontainer-from-the-labelobject/5528)

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**Author:** [@SummerZ2020](https://discourse.itk.org/u/SummerZ2020)\
**Replies:** 2\
**Last updated:** [November 29, 2022, 8:33am UTC](https://discourse.itk.org/t/how-to-get-m-linecontainer-from-the-labelobject/5528 "2022-11-29T08:33:45Z")

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hello, Thank you for the great work, it helps me a lot. currently, I need the points positions in the m\_LineContainer of labelObject? As I know, m\_LineContainer is private variable, how can I get it from my code? Thanks…

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## [How to understand the world coordinate of DSA?](https://discourse.itk.org/t/how-to-understand-the-world-coordinate-of-dsa/5490)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 10\
**Last updated:** [November 28, 2022, 2:16pm UTC](https://discourse.itk.org/t/how-to-understand-the-world-coordinate-of-dsa/5490 "2022-11-28T14:16:01Z")

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DSA (digital subtraction angiography) have two important tags: (0018, 1110) Distance Source to Detector (0018, 1111) Distance Source to Patient The DSA image is perspective projection to an object, likes: where S i…

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## [WriteImage output not consistent](https://discourse.itk.org/t/writeimage-output-not-consistent/5526)

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**Author:** [@Toby-Jackson](https://discourse.itk.org/u/Toby-Jackson)\
**Replies:** 4\
**Last updated:** [November 28, 2022, 12:54pm UTC](https://discourse.itk.org/t/writeimage-output-not-consistent/5526 "2022-11-28T12:54:46Z")

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I’ve written a script that iterates over some images, and analyses those images with different parameter sets, saving the output to file. When running the code the output saved to file is inconsistent, and sometimes look…

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## [There are deviations between generated DRR image and corresponding EPID image](https://discourse.itk.org/t/there-are-deviations-between-generated-drr-image-and-corresponding-epid-image/5522)

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**Author:** [@suzume](https://discourse.itk.org/u/suzume)\
**Replies:** 5\
**Last updated:** [November 25, 2022, 2:42pm UTC](https://discourse.itk.org/t/there-are-deviations-between-generated-drr-image-and-corresponding-epid-image/5522 "2022-11-25T14:42:02Z")

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I want to generate the DRR image from the CT and register it with the corresponding EPID image. However, there are always deviations between the generated DRR image and its corresponding EPID image. The EPID is obtained …

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## [AttributeError: module ‘itk’ has no attribute ‘DescoteauxSheetnessImageFilter’](https://discourse.itk.org/t/attributeerror-module-itk-has-no-attribute-descoteauxsheetnessimagefilter/5524)

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**Author:** [@Konohana](https://discourse.itk.org/u/Konohana)\
**Replies:** 2\
**Last updated:** [November 24, 2022, 4:35pm UTC](https://discourse.itk.org/t/attributeerror-module-itk-has-no-attribute-descoteauxsheetnessimagefilter/5524 "2022-11-24T16:35:59Z")

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Hey there I am trying to use the SheetnessImageFilter from itk in python. However I am getting an AttributeError for this particular filter, others work fine. I saw in another thread that it could be due to incompatibil…

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## [Viewer: Show 3D numpy array with colours specified by array](https://discourse.itk.org/t/viewer-show-3d-numpy-array-with-colours-specified-by-array/5439)

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**Author:** [@Kevin\_Sweeney](https://discourse.itk.org/u/Kevin_Sweeney)\
**Replies:** 5\
**Last updated:** [November 24, 2022, 2:52am UTC](https://discourse.itk.org/t/viewer-show-3d-numpy-array-with-colours-specified-by-array/5439 "2022-11-24T02:52:07Z")

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I have a 3D numpy array (shape = (224, 224, 3)) which defines the RGB values at each pixel (uint8). How can I use ikwidgets.view() method to show this array using the RBG colours instead of a colourmap? Code: view(arr…

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## [Connected components in python](https://discourse.itk.org/t/connected-components-in-python/1658)

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**Author:** [@Krishna\_Nanda](https://discourse.itk.org/u/Krishna_Nanda)\
**Replies:** 12\
**Last updated:** [November 23, 2022, 4:49pm UTC](https://discourse.itk.org/t/connected-components-in-python/1658 "2022-11-23T16:49:58Z")

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Hello all, I am very new to SimpleITK. I am trying to get all the connected components from a 3D binary image (including the pixel locations of the various components) with multiple masks. The 3D binary image is of “Ima…

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## [How to create a binary mask from coordinates (indexes or physical)](https://discourse.itk.org/t/how-to-create-a-binary-mask-from-coordinates-indexes-or-physical/4611)

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**Author:** [@Ervis](https://discourse.itk.org/u/Ervis)\
**Replies:** 5\
**Last updated:** [November 23, 2022, 4:22pm UTC](https://discourse.itk.org/t/how-to-create-a-binary-mask-from-coordinates-indexes-or-physical/4611 "2022-11-23T16:22:21Z")

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Hi I am new to ITK , I am using SimpleITK in C#. I have planar closed contour , a set of coordinates. What I need to do is create a binary mask with the same dimensions spacing and origin as the original ITK Image. I …

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## [Trouble viewing PET image (mha file) in SimpleITK](https://discourse.itk.org/t/trouble-viewing-pet-image-mha-file-in-simpleitk/5507)

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**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 2\
**Last updated:** [November 23, 2022, 6:41am UTC](https://discourse.itk.org/t/trouble-viewing-pet-image-mha-file-in-simpleitk/5507 "2022-11-23T06:41:16Z")

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Hello, I am using the following python code to view a PET and an MR image. fixed\_image = sitk.ReadImage("PET.mha", sitk.sitkFloat64) moving\_image = sitk.ReadImage("MR.mha", sitk.sitkFloat64) point\_acquisition\_interfac…

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## [how to view mha file in Python](https://discourse.itk.org/t/how-to-view-mha-file-in-python/5515)

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**Author:** [@Uljibuh](https://discourse.itk.org/u/Uljibuh)\
**Replies:** 2\
**Last updated:** [November 22, 2022, 6:16pm UTC](https://discourse.itk.org/t/how-to-view-mha-file-in-python/5515 "2022-11-22T18:16:26Z")

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Hi all, a beginner here, I am working on prostate cancer 3D dataset using deep learning, I can open these 3D files using Fiji, how I can open in python using SimpleITK ? do I need to convert these file into specific f…

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## [GetDRRSiddonJacobsRayTracing](https://discourse.itk.org/t/getdrrsiddonjacobsraytracing/5512)

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**Author:** [@YuanYang\_Deng](https://discourse.itk.org/u/YuanYang_Deng)\
**Replies:** 3\
**Last updated:** [November 22, 2022, 12:23am UTC](https://discourse.itk.org/t/getdrrsiddonjacobsraytracing/5512 "2022-11-22T00:23:34Z")

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I want to convert 3D CT images into X-ray images using DRR technology. But I don’t know how to use and run this algorithm. Did anyone run it successfully? Can you talk about how you work? https://github.com/InsightSoftw…

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## [Where is ITKConfig.cmake in ITK-5.2.1?](https://discourse.itk.org/t/where-is-itkconfig-cmake-in-itk-5-2-1/5510)

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**Author:** [@Carles\_Lopez](https://discourse.itk.org/u/Carles_Lopez)\
**Replies:** 1\
**Last updated:** [November 21, 2022, 6:14pm UTC](https://discourse.itk.org/t/where-is-itkconfig-cmake-in-itk-5-2-1/5510 "2022-11-21T18:14:08Z")

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Hello to everyone. I’ve installed itk-5.2.1 with pip in an anaconda environment on Python 3.9. On the other hand, I’m trying to run CMake. I’m asked about the directory where ITKConfig.cmake or itk-config. cmake is loc…

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## [Gantry rotation when generate DRR](https://discourse.itk.org/t/gantry-rotation-when-generate-drr/5500)

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**Author:** [@suzume](https://discourse.itk.org/u/suzume)\
**Replies:** 4\
**Last updated:** [November 21, 2022, 6:12pm UTC](https://discourse.itk.org/t/gantry-rotation-when-generate-drr/5500 "2022-11-21T18:12:34Z")

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I want to rotate the gantry and couch when generating the DRR image. An Euler transformation is used to rotate the input volume to simulate the couch rotation. What else can I use to rotate the gantry? Can I use Euler tr…

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## [How to convert .stl file to mesh data](https://discourse.itk.org/t/how-to-convert-stl-file-to-mesh-data/5488)

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**Author:** [@Zijian\_Hu](https://discourse.itk.org/u/Zijian_Hu)\
**Replies:** 11\
**Last updated:** [November 21, 2022, 2:14pm UTC](https://discourse.itk.org/t/how-to-convert-stl-file-to-mesh-data/5488 "2022-11-21T14:14:19Z")

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Hi, I am trying to convert a .stl file to mesh data. It seems there is no direct way to implement it. So, my idea is first convert the file to a temporary .vtk file and then using itk.meshread() to get the mesh data. Ho…

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## [How do I get a Pointer to an Image](https://discourse.itk.org/t/how-do-i-get-a-pointer-to-an-image/5497)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 6\
**Last updated:** [November 19, 2022, 2:04am UTC](https://discourse.itk.org/t/how-do-i-get-a-pointer-to-an-image/5497 "2022-11-19T02:04:42Z")

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Hi folks, I am trying to use an Advection Image in the GeodesicActiveCountour segmentation. I think the advection image must be a pointer to an pointer to a vector image. In my case the program asks for a: itk::Image\<i…

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## [Read CT volume compatible to nibabel orientation using SimpleITK](https://discourse.itk.org/t/read-ct-volume-compatible-to-nibabel-orientation-using-simpleitk/5254)

<div class="topic-metadata">

**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 3\
**Last updated:** [November 18, 2022, 12:06pm UTC](https://discourse.itk.org/t/read-ct-volume-compatible-to-nibabel-orientation-using-simpleitk/5254 "2022-11-18T12:06:01Z")

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I want to read the CT volume from simpleITK with compatible to nibabel. When I read the CT volume using nibabel, the orientation (i.e. LAS), image origin, spacing and start, and ending physical points are output as seen…

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## [What is the code for sitk.Tramsform()?](https://discourse.itk.org/t/what-is-the-code-for-sitk-tramsform/5495)

<div class="topic-metadata">

**Author:** [@pranoy-ray](https://discourse.itk.org/u/pranoy-ray)\
**Replies:** 8\
**Last updated:** [November 17, 2022, 9:13pm UTC](https://discourse.itk.org/t/what-is-the-code-for-sitk-tramsform/5495 "2022-11-17T21:13:55Z")

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def make\_isotropicBCC( image, interpolator=sitk.sitkLinear, spacing=None, default\_value=0, standardize\_axes=False,): original\_spacing = image.GetSpacing() # Make image isotropic via r…

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