# Latest

**URL:** https://discourse.itk.org/latest.md?page=71

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

**Page:** 72

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## [LabelIntensityStatisticsImageFilter error](https://discourse.itk.org/t/labelintensitystatisticsimagefilter-error/2852)

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**Author:** [@flaviu2](https://discourse.itk.org/u/flaviu2)\
**Replies:** 7\
**Last updated:** [March 19, 2020, 4:33pm UTC](https://discourse.itk.org/t/labelintensitystatisticsimagefilter-error/2852 "2020-03-19T16:33:15Z")

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I have tried the following code: sitk::Image imgTemp(img); sitk::Image cc = sitk::ConnectedComponent(imgTemp, true); sitk::LabelIntensityStatisticsImageFilter statistics; statistics.Execute(cc, imgTemp); std::vector\<int…

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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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## [Can't find "ITKVtkGlueExport.h" file included in "QuickView.h"](https://discourse.itk.org/t/cant-find-itkvtkglueexport-h-file-included-in-quickview-h/2854)

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**Author:** [@Come](https://discourse.itk.org/u/Come)\
**Replies:** 3\
**Last updated:** [March 19, 2020, 5:37pm UTC](https://discourse.itk.org/t/cant-find-itkvtkglueexport-h-file-included-in-quickview-h/2854 "2020-03-19T17:37:41Z")

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Hi, I am trying to use the QuickView object to display a 3d image but I can’t find the ITKVtkGlueExport.h file anywhere even though it’s included in the QuickView.h file. Am I missing something? Côme

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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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## [Read image and metada from folder full of dicom image](https://discourse.itk.org/t/read-image-and-metada-from-folder-full-of-dicom-image/2841)

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**Author:** [@drcjaudet](https://discourse.itk.org/u/drcjaudet)\
**Replies:** 4\
**Last updated:** [March 19, 2020, 3:20pm UTC](https://discourse.itk.org/t/read-image-and-metada-from-folder-full-of-dicom-image/2841 "2020-03-19T15:20:56Z")

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Hello high tea key, i am trying to read image and metadata from a folder with the following code. It succeed to open the image but find no metadata and i sure they are. How can i access to them? from \_main\_import vtk,…

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## [constraining parameters during optimization](https://discourse.itk.org/t/constraining-parameters-during-optimization/2848)

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**Author:** [@reox](https://discourse.itk.org/u/reox)\
**Replies:** 7\
**Last updated:** [March 19, 2020, 12:55pm UTC](https://discourse.itk.org/t/constraining-parameters-during-optimization/2848 "2020-03-19T12:55:07Z")

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For example, I’m using the Similarity2DTransform. Here, I would like to enforce that the scale must be non-zero and positive, however I would like to allow for negative translation. Is it correct, that the only optimize…

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## [How to create an atlas based on PET image](https://discourse.itk.org/t/how-to-create-an-atlas-based-on-pet-image/2853)

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**Author:** [@drcjaudet](https://discourse.itk.org/u/drcjaudet)\
**Replies:** 0\
**Last updated:** [March 19, 2020, 12:47pm UTC](https://discourse.itk.org/t/how-to-create-an-atlas-based-on-pet-image/2853 "2020-03-19T12:47:05Z")

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Hello TTK community, Here a little bit of a technical question. The goal is to create an atlas image based on several whole body PET image (starting from 100 ot finally 10000) in an efficient way. Now i register the i…

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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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## [IO in python module](https://discourse.itk.org/t/io-in-python-module/2846)

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**Author:** [@simon.rit](https://discourse.itk.org/u/simon.rit)\
**Replies:** 5\
**Last updated:** [March 18, 2020, 5:47pm UTC](https://discourse.itk.org/t/io-in-python-module/2846 "2020-03-18T17:47:33Z")

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I have started to work on the wrapping of IO in RTK: There is something which is not clear to me. When working with C++, I can register IO factories so that this is quite transparent for the user, the adequate ImageI…

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## [Rotation angle of Z-axis](https://discourse.itk.org/t/rotation-angle-of-z-axis/2817)

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**Author:** [@spinicist](https://discourse.itk.org/u/spinicist)\
**Replies:** 3\
**Last updated:** [March 18, 2020, 4:55pm UTC](https://discourse.itk.org/t/rotation-angle-of-z-axis/2817 "2020-03-18T16:55:12Z")

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Hello, I have an itk::Transform (specifically an itk::AffineTransform). I would like to know how much this transform rotates the Z-axis - i.e. the angle between (0,0,1) and the result of applying the transform to (0,0,1…

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## [Can ITK extract the skeleton for a 3D mask?](https://discourse.itk.org/t/can-itk-extract-the-skeleton-for-a-3d-mask/2816)

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**Author:** [@qiang-zhang-neu](https://discourse.itk.org/u/qiang-zhang-neu)\
**Replies:** 8\
**Last updated:** [March 18, 2020, 1:23pm UTC](https://discourse.itk.org/t/can-itk-extract-the-skeleton-for-a-3d-mask/2816 "2020-03-18T13:23:58Z")

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Now, I need to extract the skeleton for a 3D mask. And I find the itkBinaryThinningImageFilter is useful for 2D mask, and it doesn’t work for a 3D mask. Can ITK extract the skeleton for a 3D mask?

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## [sitk::Image adding / multiplying](https://discourse.itk.org/t/sitk-image-adding-multiplying/2845)

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**Author:** [@flaviu2](https://discourse.itk.org/u/flaviu2)\
**Replies:** 3\
**Last updated:** [March 18, 2020, 11:26am UTC](https://discourse.itk.org/t/sitk-image-adding-multiplying/2845 "2020-03-18T11:26:34Z")

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Hello. I saw here a little python code: https://itk.org/SimpleITKDoxygen/html/Python\_2BoarderSegmentation\_8py-example.html And I want to try it, in C++. How can convert this code: image = image \* ~boundary image = imag…

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## [GraphCutSegmentation in SimpleITK](https://discourse.itk.org/t/graphcutsegmentation-in-simpleitk/2844)

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**Author:** [@flaviu2](https://discourse.itk.org/u/flaviu2)\
**Replies:** 0\
**Last updated:** [March 17, 2020, 7:31pm UTC](https://discourse.itk.org/t/graphcutsegmentation-in-simpleitk/2844 "2020-03-17T19:31:58Z")

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Hello everyone. Is there any graph cut segmentation implemented into SimpleITK library ? As far as understood, is very suitable for bone segmentation, and because I didn’t found until now any suitable solution in SimpleI…

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## [ImageSeries Reader reads dicom series in reverse order by default?](https://discourse.itk.org/t/imageseries-reader-reads-dicom-series-in-reverse-order-by-default/2491)

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**Author:** [@Jigabytes](https://discourse.itk.org/u/Jigabytes)\
**Replies:** 12\
**Last updated:** [March 17, 2020, 3:43pm UTC](https://discourse.itk.org/t/imageseries-reader-reads-dicom-series-in-reverse-order-by-default/2491 "2020-03-17T15:43:18Z")

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Hi I am trying to read CT scan dicom series using Simple ITK ImageSeriesReader() In order verify each image slice I also load the CT scan in osirix image viewer. After reading from series reader when I load sample slic…

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## [ITK DCMTK external build fails](https://discourse.itk.org/t/itk-dcmtk-external-build-fails/2834)

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**Author:** [@tim-evain](https://discourse.itk.org/u/tim-evain)\
**Replies:** 3\
**Last updated:** [March 17, 2020, 3:34pm UTC](https://discourse.itk.org/t/itk-dcmtk-external-build-fails/2834 "2020-03-17T15:34:12Z")

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Hello folks, I’m currently building docker images for test automation and I’m facing an issue with the ITK-patched DCMTK external project. During the build I get this error (I’m building an image based on ubuntu 20.04 w…

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## [ImageSeriesWriter in rare cases writes image position (0020,0032) incorrectly](https://discourse.itk.org/t/imageserieswriter-in-rare-cases-writes-image-position-0020-0032-incorrectly/2839)

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**Author:** [@svg](https://discourse.itk.org/u/svg)\
**Replies:** 0\
**Last updated:** [March 17, 2020, 9:32am UTC](https://discourse.itk.org/t/imageserieswriter-in-rare-cases-writes-image-position-0020-0032-incorrectly/2839 "2020-03-17T09:32:10Z")

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Hi Over the last year or so I have, on some machines using ITK, run into troubles regarding the image position header being written incorrectly. Short example of the problem: I use the ImageSeriesWriter to write 2D im…

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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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## [Hackathon following WBIR](https://discourse.itk.org/t/hackathon-following-wbir/770)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 6\
**Last updated:** [March 16, 2020, 2:40pm UTC](https://discourse.itk.org/t/hackathon-following-wbir/770 "2020-03-16T14:40:39Z")

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Leiden, The Netherlands June 28 & 29, 2018 Website: wbir2018.nl New: Call for 1-page abstracts: deadline April 1, 2018 New: Continuous Registration Challenge – Participate! New: Post-WBIR Hackathon Dear colleagues, …

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## [ITKExamples Hackathon at ISBI Iowa 2020](https://discourse.itk.org/t/itkexamples-hackathon-at-isbi-iowa-2020/2788)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 1\
**Last updated:** [March 13, 2020, 3:01pm UTC](https://discourse.itk.org/t/itkexamples-hackathon-at-isbi-iowa-2020/2788 "2020-03-13T15:01:02Z")

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At ISBI 2020, @dzenanz, @hjmjohnson, and I will organize a hackathon to update and add new ITKExamples. We will update the examples to bring them up to speed with ITK 5.1, put finishing touches on the Wiki Examples migra…

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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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## [Free Biomedical Image Analysis and Visualization 3-day Course: March 24-26, 2020, Carrboro, NC, USA](https://discourse.itk.org/t/free-biomedical-image-analysis-and-visualization-3-day-course-march-24-26-2020-carrboro-nc-usa/2620)

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**Author:** [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Replies:** 4\
**Last updated:** [March 13, 2020, 2:19am UTC](https://discourse.itk.org/t/free-biomedical-image-analysis-and-visualization-3-day-course-march-24-26-2020-carrboro-nc-usa/2620 "2020-03-13T02:19:06Z")

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Kitware has organized another free 3-day biomedical image analysis and visualization course to be held March 24-26, 2020, at Kitware’s Carrboro, NC, USA office. The course is designed for clinical researchers and techno…

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## [Registering two Images](https://discourse.itk.org/t/registering-two-images/2821)

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**Author:** [@cntontis](https://discourse.itk.org/u/cntontis)\
**Replies:** 3\
**Last updated:** [March 12, 2020, 2:06pm UTC](https://discourse.itk.org/t/registering-two-images/2821 "2020-03-12T14:06:55Z")

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Hello everyone, I am new with Image Registration and i am trying to register images similar to the following ones. In most cases it works really well but in cases like this the algorithm stops after a few steps. …

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## [Extract image using threshold](https://discourse.itk.org/t/extract-image-using-threshold/2757)

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**Author:** [@osemmler](https://discourse.itk.org/u/osemmler)\
**Replies:** 10\
**Last updated:** [March 10, 2020, 8:45pm UTC](https://discourse.itk.org/t/extract-image-using-threshold/2757 "2020-03-10T20:45:25Z")

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Hello, can you advise me the most efficient combination of filters to extract region of image based on threshold value? (ie reduce the image by margins that are below the defined threshold value)

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## [Rotating a mapper with euler transform.](https://discourse.itk.org/t/rotating-a-mapper-with-euler-transform/2809)

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**Author:** [@Jose\_Alejandro\_Garni](https://discourse.itk.org/u/Jose_Alejandro_Garni)\
**Replies:** 3\
**Last updated:** [March 10, 2020, 7:45pm UTC](https://discourse.itk.org/t/rotating-a-mapper-with-euler-transform/2809 "2020-03-10T19:45:04Z")

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Hi guys! im trying to apply euler 3d transformation matrix, to a mapper (a segmentation archive) that i have in dicom format. but when i apply the resampling filter, it seems to smootj the image instead of rotating it… …

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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 5.1 Release Candidate 2 available for testing](https://discourse.itk.org/t/itk-5-1-release-candidate-2-available-for-testing/2803)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 3\
**Last updated:** [March 10, 2020, 9:53am UTC](https://discourse.itk.org/t/itk-5-1-release-candidate-2-available-for-testing/2803 "2020-03-10T09:53:02Z")

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We are happy to announce the Insight Toolkit (ITK) 5.1 Release Candidate 2 is available for testing! :tada: ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and r…

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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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## [register stack of images](https://discourse.itk.org/t/register-stack-of-images/2794)

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**Author:** [@kayarre](https://discourse.itk.org/u/kayarre)\
**Replies:** 3\
**Last updated:** [March 7, 2020, 4:27pm UTC](https://discourse.itk.org/t/register-stack-of-images/2794 "2020-03-07T16:27:12Z")

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I have mention this data stack I have before, but just had an epiphany and am looking for additional insight. I wan to register a sparse stack of images to a 3d volume. fixed 3d volume. I have a set of ordered 2d image…

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## [Account for non-uniform spacing](https://discourse.itk.org/t/account-for-non-uniform-spacing/2797)

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**Author:** [@trypag](https://discourse.itk.org/u/trypag)\
**Replies:** 8\
**Last updated:** [March 7, 2020, 4:06pm UTC](https://discourse.itk.org/t/account-for-non-uniform-spacing/2797 "2020-03-07T16:06:51Z")

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Hello, When loading a DICOM series in Slicer I noticed a warning related to the spacing of the images, so I manually checked if the spacing was the same between each slices, it’s not. Converting the DICOM series with S…

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## [FFT mismatch ITK/matlab](https://discourse.itk.org/t/fft-mismatch-itk-matlab/2776)

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**Author:** [@Jonas](https://discourse.itk.org/u/Jonas)\
**Replies:** 11\
**Last updated:** [March 6, 2020, 4:53pm UTC](https://discourse.itk.org/t/fft-mismatch-itk-matlab/2776 "2020-03-06T16:53:28Z")

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Hi, I would like to know how to match the FFT implementation of matlab fftn function using ITK. I tried both itkForwardFFTImageFilter alone and the PadIlmageFilter + ForwardFFTImageFilter. taken from https://itk.org/…

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