# Uncategorized

**URL:** https://discourse.itk.org/c/uncategorized/1.md?no_subcategories=false&page=10

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

**Page:** 11

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## [Deformable Registration](https://discourse.itk.org/t/deformable-registration/2955)

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**Author:** [@srbn.ghosh89](https://discourse.itk.org/u/srbn.ghosh89)\
**Replies:** 3\
**Last updated:** [April 17, 2020, 3:05pm UTC](https://discourse.itk.org/t/deformable-registration/2955 "2020-04-17T15:05:33Z")

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Hi, I am trying to do a deformable registration after doing a landmark-based registration between a triangular simplex mesh and CT image. In the snapshot, after using a landmark-based registration I got the registere…

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## [Nifti (RPI orientation) file exported to DICOM - wrong orientation](https://discourse.itk.org/t/nifti-rpi-orientation-file-exported-to-dicom-wrong-orientation/1612)

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**Author:** [@mihail.isakov](https://discourse.itk.org/u/mihail.isakov)\
**Replies:** 10\
**Last updated:** [April 17, 2020, 11:40am UTC](https://discourse.itk.org/t/nifti-rpi-orientation-file-exported-to-dicom-wrong-orientation/1612 "2020-04-17T11:40:30Z")

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Hello, Just FYI. experiment: take this Nifti file https://nifti.nimh.nih.gov/nifti-1/data/avg152T1\_LR\_nifti.nii.gz/file\_view and export to DICOM result is horrible wrong. It happens because GDCM uses Multi Frame G…

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## [why the running time of CPU and GPU are same, while i use itkRWSegmentationFilter and itkCudaRWSegmentationFilter](https://discourse.itk.org/t/why-the-running-time-of-cpu-and-gpu-are-same-while-i-use-itkrwsegmentationfilter-and-itkcudarwsegmentationfilter/2959)

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**Author:** [@KaryLiang](https://discourse.itk.org/u/KaryLiang)\
**Replies:** 0\
**Last updated:** [April 17, 2020, 3:02am UTC](https://discourse.itk.org/t/why-the-running-time-of-cpu-and-gpu-are-same-while-i-use-itkrwsegmentationfilter-and-itkcudarwsegmentationfilter/2959 "2020-04-17T03:02:31Z")

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code from:GitHub - enricperera/itkRWSegmentationFilter: ITK-like filter for image segmentation using the random walker algorithm I run the code itkRWSegmentationFilter successful in CPU, but there has some error when i …

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## [Negation after mask operation](https://discourse.itk.org/t/negation-after-mask-operation/2884)

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**Author:** [@flaviu2](https://discourse.itk.org/u/flaviu2)\
**Replies:** 4\
**Last updated:** [April 2, 2020, 10:40am UTC](https://discourse.itk.org/t/negation-after-mask-operation/2884 "2020-04-02T10:40:03Z")

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I have loaded a CBCT into sitk::Image. And I ran: sitk::Image imgTemp(imgOrg); sitk::Image threshold = sitk::BinaryThreshold(imgTemp, 2000, 3600); // let only teeth (tough bones) sitk::MaskImageFilter mask; and I see …

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## [Does simple ITK (python) offers all the functionalities as the C++ ITK?](https://discourse.itk.org/t/does-simple-itk-python-offers-all-the-functionalities-as-the-c-itk/2890)

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**Author:** [@machadoL](https://discourse.itk.org/u/machadoL)\
**Replies:** 6\
**Last updated:** [April 1, 2020, 9:10pm UTC](https://discourse.itk.org/t/does-simple-itk-python-offers-all-the-functionalities-as-the-c-itk/2890 "2020-04-01T21:10:12Z")

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## [Correlation of two images](https://discourse.itk.org/t/correlation-of-two-images/2815)

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**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 5\
**Last updated:** [March 31, 2020, 5:12pm UTC](https://discourse.itk.org/t/correlation-of-two-images/2815 "2020-03-31T17:12:33Z")

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How do I perform the correlation between two patches that I extracted from an image? I have extracted two patches and saved them into two different images. Now I just want to perform correlation between them. There is n…

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## [Advice on registering noisy head CT on template](https://discourse.itk.org/t/advice-on-registering-noisy-head-ct-on-template/2849)

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**Author:** [@trypag](https://discourse.itk.org/u/trypag)\
**Replies:** 12\
**Last updated:** [March 20, 2020, 7:02pm UTC](https://discourse.itk.org/t/advice-on-registering-noisy-head-ct-on-template/2849 "2020-03-20T19:02:48Z")

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Hello, I am trying to register a head CT (with headset) on a head CT template. The presence of a headset is challenging the whole registration step (I think). It can eventually succeed if I wait long enough. I am looki…

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## [The time of converting cpu image to gpu image is too long](https://discourse.itk.org/t/the-time-of-converting-cpu-image-to-gpu-image-is-too-long/2836)

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**Author:** [@qiang-zhang-neu](https://discourse.itk.org/u/qiang-zhang-neu)\
**Replies:** 7\
**Last updated:** [March 20, 2020, 1:18am UTC](https://discourse.itk.org/t/the-time-of-converting-cpu-image-to-gpu-image-is-too-long/2836 "2020-03-20T01:18:26Z")

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In my project, I need to convert the itk::Image to itk::GPUImage. However, I find the time is too long (~ 3s) in release version. The code is: start1 = clock(); CPUTOGPUImageFilterPointer cpuToGpuImageFilter = CPUT…

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## [Whole Image binning for GLCM](https://discourse.itk.org/t/whole-image-binning-for-glcm/2835)

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**Author:** [@sarthakpati](https://discourse.itk.org/u/sarthakpati)\
**Replies:** 10\
**Last updated:** [March 19, 2020, 3:59pm UTC](https://discourse.itk.org/t/whole-image-binning-for-glcm/2835 "2020-03-19T15:59:30Z")

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Hi, I am trying to extract GLCM matrix from an image and mask using itk::Statistics::ScalarImageToCooccurrenceMatrixFilter. I wanted to verify how the quantization happens on the provided binning information: Only the…

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## [Double brackets \[\[ITK\]\] in the subject of email notifications](https://discourse.itk.org/t/double-brackets-itk-in-the-subject-of-email-notifications/2850)

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**Author:** [@phcerdan](https://discourse.itk.org/u/phcerdan)\
**Replies:** 2\
**Last updated:** [March 18, 2020, 8:16pm UTC](https://discourse.itk.org/t/double-brackets-itk-in-the-subject-of-email-notifications/2850 "2020-03-18T20:16:26Z")

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Just wondering why the email notifications have changed to have double brackets: \[\[ITK\]\] instead of just the standard \[ITK\] in their subject.

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## [Reading a 4D volume (3D + time) from a dcm format and plotting it](https://discourse.itk.org/t/reading-a-4d-volume-3d-time-from-a-dcm-format-and-plotting-it/2832)

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**Author:** [@bjce](https://discourse.itk.org/u/bjce)\
**Replies:** 7\
**Last updated:** [March 16, 2020, 4:22pm UTC](https://discourse.itk.org/t/reading-a-4d-volume-3d-time-from-a-dcm-format-and-plotting-it/2832 "2020-03-16T16:22:29Z")

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Hi everyone. I have a DICOM from echocardiography which is a 4D Volume (3D space + time) that I could save in a .dcm format. I want to use SimpleITK to open it and plot it. Is it possible to read the .dcm file and plot i…

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## [How to compute & plot hostogram of dicom images?](https://discourse.itk.org/t/how-to-compute-plot-hostogram-of-dicom-images/2822)

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**Author:** [@Pooja\_Virkar](https://discourse.itk.org/u/Pooja_Virkar)\
**Replies:** 5\
**Last updated:** [March 13, 2020, 1:37pm UTC](https://discourse.itk.org/t/how-to-compute-plot-hostogram-of-dicom-images/2822 "2020-03-13T13:37:19Z")

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Hello, I want to compute the histogram of dicom images and then plot that graph. I tried to use the example from https://itk.org/Doxygen/html/SphinxExamples\_2src\_2Numerics\_2Statistics\_2ComputeHistogramFromGrayscaleIma…

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## [looking to process a CAD file like a medical image... what is the best file format, between igs, x\_t or sat...?](https://discourse.itk.org/t/looking-to-process-a-cad-file-like-a-medical-image-what-is-the-best-file-format-between-igs-x-t-or-sat/2813)

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**Author:** [@MichelODU](https://discourse.itk.org/u/MichelODU)\
**Replies:** 4\
**Last updated:** [March 10, 2020, 3:54pm UTC](https://discourse.itk.org/t/looking-to-process-a-cad-file-like-a-medical-image-what-is-the-best-file-format-between-igs-x-t-or-sat/2813 "2020-03-10T15:54:24Z")

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Dear ITK users, I would like to process a CAD file like a medical tomographic image, e.g. compute a distance map from the boundary towards a medial axis. It appears that the company making the file available to me can g…

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## [ITK libpng version](https://discourse.itk.org/t/itk-libpng-version/2802)

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**Author:** [@Fijoy\_Vadakkumpadan](https://discourse.itk.org/u/Fijoy_Vadakkumpadan)\
**Replies:** 2\
**Last updated:** [March 9, 2020, 4:00pm UTC](https://discourse.itk.org/t/itk-libpng-version/2802 "2020-03-09T16:00:57Z")

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Hello, What version of libpng does ITK use? I’m trying to resolve the (security) vulnerabilities associated with libpng by updating ITK to the latest version. But looking at the source (Modules/ThirdParty/PNG/itkpng/pn…

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## [Do segmentation on dicom volume](https://discourse.itk.org/t/do-segmentation-on-dicom-volume/2695)

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**Author:** [@flaviu2](https://discourse.itk.org/u/flaviu2)\
**Replies:** 5\
**Last updated:** [March 5, 2020, 3:53pm UTC](https://discourse.itk.org/t/do-segmentation-on-dicom-volume/2695 "2020-03-05T15:53:19Z")

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I have found some similar post here, but they are not clear me enough, so forgive me if I put here a too simple question. I have a VC++ app that read dicom images (with VTK DICOM library). I am using for that vtkDICOMRe…

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## [Simple test for SimpleITK to VTK conversion](https://discourse.itk.org/t/simple-test-for-simpleitk-to-vtk-conversion/2752)

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**Author:** [@flaviu2](https://discourse.itk.org/u/flaviu2)\
**Replies:** 5\
**Last updated:** [February 27, 2020, 2:40pm UTC](https://discourse.itk.org/t/simple-test-for-simpleitk-to-vtk-conversion/2752 "2020-02-27T14:40:06Z")

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I have tried a simple test to check my conversion from SimpleITK to VTK: // visualize vtkVolume color ... /// convert VTK ro SimpleITK sitk::Image img = importer.Execute(); //////////////////////////////////////////// i…

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## [Why sitk.GetDirection() is not the same with '0020|0037' ?](https://discourse.itk.org/t/why-sitk-getdirection-is-not-the-same-with-0020-0037/2755)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 3\
**Last updated:** [February 23, 2020, 2:04am UTC](https://discourse.itk.org/t/why-sitk-getdirection-is-not-the-same-with-0020-0037/2755 "2020-02-23T02:04:28Z")

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In my thought, I think both sitk.GetDirection() and ‘0020|0037’ indicate the patient orientation. However, I find they are different. Firstly, I get the direction: \>\>\> sitkImage = sitk.ReadImage('IM\_0177') \>\>\> sitkImag…

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## [Deformable Registration and .vtk file Help](https://discourse.itk.org/t/deformable-registration-and-vtk-file-help/2699)

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**Author:** [@ShaneKirkbride](https://discourse.itk.org/u/ShaneKirkbride)\
**Replies:** 12\
**Last updated:** [February 19, 2020, 1:54pm UTC](https://discourse.itk.org/t/deformable-registration-and-vtk-file-help/2699 "2020-02-19T13:54:18Z")

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I have a set of similar DICOM files. I need to convert them to a 3D mesh and then register them. Then I need to transform the meshes so they are both on the same coordinate system. After this I need to calculate the area…

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## [Compile SimpleITK](https://discourse.itk.org/t/compile-simpleitk/2709)

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**Author:** [@flaviu2](https://discourse.itk.org/u/flaviu2)\
**Replies:** 20\
**Last updated:** [February 14, 2020, 9:44am UTC](https://discourse.itk.org/t/compile-simpleitk/2709 "2020-02-14T09:44:45Z")

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I want to signal a possible malfunction while compiling SimpleITK. I intend to use SimpleITK into VC++ project on windows, developing environment VS2017. If I download the source code from here: http://www.simpleitk.or…

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## [python-itk: GPU ](https://discourse.itk.org/t/python-itk-gpu/2707)

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**Author:** [@qiang-zhang-neu](https://discourse.itk.org/u/qiang-zhang-neu)\
**Replies:** 1\
**Last updated:** [February 12, 2020, 4:17pm UTC](https://discourse.itk.org/t/python-itk-gpu/2707 "2020-02-12T16:17:36Z")

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I want to use GPU based itk for image registration. I compile itk from source code, and the ITK\_USE\_GPU is set to ON. The compiling is OK. The itk can be imported in python: import itk itk.Image\[itk.F, 3\] \<class ‘…

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## [Handle errors on SimpleITK](https://discourse.itk.org/t/handle-errors-on-simpleitk/2698)

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**Author:** [@flaviu2](https://discourse.itk.org/u/flaviu2)\
**Replies:** 3\
**Last updated:** [February 10, 2020, 3:41pm UTC](https://discourse.itk.org/t/handle-errors-on-simpleitk/2698 "2020-02-10T15:41:00Z")

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Can you tell me how to handle possible errors when I run simpleitk code ? Here is an example: #include "sitkImage.h" #include "sitkCurvatureFlowImageFilter.h" #include "sitkConnectedThresholdImageFilter.h" #include "si…

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## [Incorrect Result from itk::ConnectedComponentImageFilter](https://discourse.itk.org/t/incorrect-result-from-itk-connectedcomponentimagefilter/2676)

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**Author:** [@DVigneault](https://discourse.itk.org/u/DVigneault)\
**Replies:** 3\
**Last updated:** [February 4, 2020, 4:36am UTC](https://discourse.itk.org/t/incorrect-result-from-itk-connectedcomponentimagefilter/2676 "2020-02-04T04:36:42Z")

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All– I’ve encountered what I believe to be a bug in the behavior of itk::ConnectedComponentImageFilter. In the below example, I create a 2x2x2 “Checkerboard” image, where there are 4 foreground pixels, none of which sh…

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## [ITK python SyN registration](https://discourse.itk.org/t/itk-python-syn-registration/2675)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 1\
**Last updated:** [February 3, 2020, 1:52pm UTC](https://discourse.itk.org/t/itk-python-syn-registration/2675 "2020-02-03T13:52:04Z")

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Could somebody provide an example for SyN registration method by ITK-python? I don’t know how to use this algorithm. In addition, I have compile python-ITK for GPU version, but I also cannot find an example to use GUP i…

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## [Highly concurrent SimpleITK program written in fsharp crashes a lot, and may return inconsistent images](https://discourse.itk.org/t/highly-concurrent-simpleitk-program-written-in-fsharp-crashes-a-lot-and-may-return-inconsistent-images/2575)

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**Author:** [@vincenzoml](https://discourse.itk.org/u/vincenzoml)\
**Replies:** 10\
**Last updated:** [January 31, 2020, 10:18pm UTC](https://discourse.itk.org/t/highly-concurrent-simpleitk-program-written-in-fsharp-crashes-a-lot-and-may-return-inconsistent-images/2575 "2020-01-31T22:18:17Z")

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Hi all, We are having bad problems with the VoxLogicA tool, which uses SimpleITK in a highly concurrent manner; the problems manifest themselves only on a recent machine with a 16-cores Intel Core i7 processor and 32GB…

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## [RTK users guid book, any book for RTK Reconstruction with examples](https://discourse.itk.org/t/rtk-users-guid-book-any-book-for-rtk-reconstruction-with-examples/2485)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 3\
**Last updated:** [January 24, 2020, 9:26pm UTC](https://discourse.itk.org/t/rtk-users-guid-book-any-book-for-rtk-reconstruction-with-examples/2485 "2020-01-24T21:26:46Z")

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Hi, Thank you in advance, I am looking for a RTK reconstruction 2d/3d that teaches about how to reconstruct from projections 2d/3d objects. explain the pipeline how to make things happen in RTK for different 3d reconstr…

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## [VXL & VNL doxygen](https://discourse.itk.org/t/vxl-vnl-doxygen/2618)

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**Author:** [@fhelen](https://discourse.itk.org/u/fhelen)\
**Replies:** 6\
**Last updated:** [January 17, 2020, 7:40am UTC](https://discourse.itk.org/t/vxl-vnl-doxygen/2618 "2020-01-17T07:40:26Z")

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Hello, I’m using VNL vector througth ITK for my daily work. But since today, i can’t access to VNL doxygen documentation (later https://public.kitware.com/vxl/doc/release/core/vnl/html/classvnl\_\_vector.html). It’s very…

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## [ITK wrap python compile error](https://discourse.itk.org/t/itk-wrap-python-compile-error/2606)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 2\
**Last updated:** [January 11, 2020, 10:45pm UTC](https://discourse.itk.org/t/itk-wrap-python-compile-error/2606 "2020-01-11T22:45:18Z")

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I want to compile ITK from source and wrap with python. But the following bug happen: My environment is: window 10 64 bit vs 2015 64 bit Python 3.7.6 (default, Jan 8 2020, 20:23:39) \[MSC v.1916 64 bit (AMD64)\] :: A…

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## [itk.org website revamp](https://discourse.itk.org/t/itk-org-website-revamp/2578)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 8\
**Last updated:** [January 7, 2020, 4:35pm UTC](https://discourse.itk.org/t/itk-org-website-revamp/2578 "2020-01-07T16:35:59Z")

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@SteveJ and the Kitware’s Communication team have contributed a major refresh to ITK’s website! :nail\_care: :tada: https://itk.org/ We are grateful to ring in 2020 with a nice website facelift. Redirects were set u…

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## [ITK website broken (at least for me?)](https://discourse.itk.org/t/itk-website-broken-at-least-for-me/2569)

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**Author:** [@Simon](https://discourse.itk.org/u/Simon)\
**Replies:** 6\
**Last updated:** [January 2, 2020, 7:45pm UTC](https://discourse.itk.org/t/itk-website-broken-at-least-for-me/2569 "2020-01-02T19:45:44Z")

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I’m not sure if this is universal, but after seeing the 5.1 announcement I went to have a look at https://itk.org/, and it is full of broken links. For example https://itk.org/ItkSoftwareGuide.pdf now gives 404 not foun…

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## [How to segment the area of interest in the image](https://discourse.itk.org/t/how-to-segment-the-area-of-interest-in-the-image/2565)

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**Author:** [@haodafeng](https://discourse.itk.org/u/haodafeng)\
**Replies:** 3\
**Last updated:** [December 25, 2019, 12:32am UTC](https://discourse.itk.org/t/how-to-segment-the-area-of-interest-in-the-image/2565 "2019-12-25T00:32:30Z")

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i am a beginer of the ITK, as the title, i want to segment the specified region of the image , how can i do?

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