# Latest **URL:** https://discourse.itk.org/latest.md?page=40 [Latest](https://discourse.itk.org/latest.md) · [Categories](https://discourse.itk.org/categories.md) · [Tags](https://discourse.itk.org/tags.md) **Page:** 41 --- ## [Select output directory for series without namesgenerator](https://discourse.itk.org/t/select-output-directory-for-series-without-namesgenerator/4864)
**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\ **Replies:** 1\ **Last updated:** [March 15, 2022, 5:19pm UTC](https://discourse.itk.org/t/select-output-directory-for-series-without-namesgenerator/4864 "2022-03-15T17:19:30Z")
How to chose the output directory to save the files from dicom series writer (2D) if I am reading from a volume 3D?I am not using not using namesgenerator but numericseriesfilenames to generate the file names for my ser… --- ## [Geodesic Active contour Level set image filter error](https://discourse.itk.org/t/geodesic-active-contour-level-set-image-filter-error/2182)
**Author:** [@Pooja\_Virkar](https://discourse.itk.org/u/Pooja_Virkar)\ **Replies:** 10\ **Last updated:** [March 15, 2022, 1:26am UTC](https://discourse.itk.org/t/geodesic-active-contour-level-set-image-filter-error/2182 "2022-03-15T01:26:59Z")
Hello, I am trying to use Geodesic Active contour Level set image filter from https://itk.org/ITKExamples/src/Segmentation/LevelSets/SegmentWithGeodesicActiveContourLevelSet/Documentation.html First I was trying to wo… --- ## [Read DICOM-RT to obtain structure volumes as arrays](https://discourse.itk.org/t/read-dicom-rt-to-obtain-structure-volumes-as-arrays/4860)
**Author:** [@RT\_newbie](https://discourse.itk.org/u/RT_newbie)\ **Replies:** 1\ **Last updated:** [March 13, 2022, 1:23pm UTC](https://discourse.itk.org/t/read-dicom-rt-to-obtain-structure-volumes-as-arrays/4860 "2022-03-13T13:23:30Z")
Hi all, What I want to do is overwriting HU value of a contoured structure in a CT image. Starting point is a CT image as DICOM sequence and a DICOM RT file for the structure set. I know how to read in the CT image an… --- ## [Deform CT image (DICOM) with DVF (mhd)](https://discourse.itk.org/t/deform-ct-image-dicom-with-dvf-mhd/4850)
**Author:** [@RT\_newbie](https://discourse.itk.org/u/RT_newbie)\ **Replies:** 4\ **Last updated:** [March 13, 2022, 7:01am UTC](https://discourse.itk.org/t/deform-ct-image-dicom-with-dvf-mhd/4850 "2022-03-13T07:01:13Z")
Hi :slight\_smile: I have a CT image as DICOM file and a deformation vector field as an .mhd file, which I want to use to deform the CT. The deformation vector field is a result from a deformable registration of the CT & … --- ## [Problem when opening a big TIF file](https://discourse.itk.org/t/problem-when-opening-a-big-tif-file/4858)
**Author:** [@Jeremie](https://discourse.itk.org/u/Jeremie)\ **Replies:** 0\ **Last updated:** [March 11, 2022, 11:38am UTC](https://discourse.itk.org/t/problem-when-opening-a-big-tif-file/4858 "2022-03-11T11:38:48Z")
Hello, I am doing mouse brains alignement to the Allen Brain Atlas. Samples are optically cleared and images are obtained on a light sheet microscope. I use ITK Elastix for registration. It works nicely on small files … --- ## [correction of gantry tilted ct image](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841)
**Author:** [@csad6517](https://discourse.itk.org/u/csad6517)\ **Replies:** 16\ **Last updated:** [March 9, 2022, 4:38pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841 "2022-03-09T16:38:30Z")
Hello, I need help by understanding the correct pipleline and determining the share factor of a gantry tilted ct dataset, so that I can apply a transform on it. I know the exact angle of the gantry over read out DICOM … --- ## [Compilation of ITK from source with Python wrappers in Arch-based systems](https://discourse.itk.org/t/compilation-of-itk-from-source-with-python-wrappers-in-arch-based-systems/4843)
**Author:** [@edgar](https://discourse.itk.org/u/edgar)\ **Replies:** 10\ **Last updated:** [March 9, 2022, 3:03pm UTC](https://discourse.itk.org/t/compilation-of-itk-from-source-with-python-wrappers-in-arch-based-systems/4843 "2022-03-09T15:03:05Z")
Compilation of ITK from source with Python wrappers in Arch-based systems Continuing the discussion from Extracting displacement fields from rigid registration: Hello! I am having long days trying to correctly compil… --- ## [dicom nrrd nifti spacing, origin mismatch.](https://discourse.itk.org/t/dicom-nrrd-nifti-spacing-origin-mismatch/4311)
**Author:** [@banikr](https://discourse.itk.org/u/banikr)\ **Replies:** 10\ **Last updated:** [March 7, 2022, 3:52pm UTC](https://discourse.itk.org/t/dicom-nrrd-nifti-spacing-origin-mismatch/4311 "2022-03-07T15:52:30Z")
Hello I am working with dicom and nrrd image file formats. Usually nrrd files are segmentations and in different spacing and origin compared to the dicoms. So my workflow is: resample the nrrd file on dicom to match di… --- ## [Get the same views of 3D dicom image](https://discourse.itk.org/t/get-the-same-views-of-3d-dicom-image/4846)
**Author:** [@tutti](https://discourse.itk.org/u/tutti)\ **Replies:** 2\ **Last updated:** [March 5, 2022, 6:48am UTC](https://discourse.itk.org/t/get-the-same-views-of-3d-dicom-image/4846 "2022-03-05T06:48:43Z")
Hello everyone, I have two 3D images (creat from 2 different registration methods, 2 images with same size (476,512,512) origin (0,0,0), direction(1,0,0,0,1,0,0,0,1)). I visualized 2 images with matplotlib (same slice)… --- ## [How to get voxel coordinates(as in ITK snap ) from vtkimage viewer from mouse click](https://discourse.itk.org/t/how-to-get-voxel-coordinates-as-in-itk-snap-from-vtkimage-viewer-from-mouse-click/4719)
**Author:** [@SREERAG\_H](https://discourse.itk.org/u/SREERAG_H)\ **Replies:** 6\ **Last updated:** [March 3, 2022, 4:25pm UTC](https://discourse.itk.org/t/how-to-get-voxel-coordinates-as-in-itk-snap-from-vtkimage-viewer-from-mouse-click/4719 "2022-03-03T16:25:34Z")
Hello, I am trying to use ITK’s region growing algorithm for medical image segmentation. So to put the seedpoint i need exact voxel coordinates of the mouse click position in my vtkimageviewer. So how can I get those vo… --- ## [How to convert a DcmDataSet of dcmtk to itk::Image ?](https://discourse.itk.org/t/how-to-convert-a-dcmdataset-of-dcmtk-to-itk-image/4839)
**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\ **Replies:** 1\ **Last updated:** [March 1, 2022, 2:43pm UTC](https://discourse.itk.org/t/how-to-convert-a-dcmdataset-of-dcmtk-to-itk-image/4839 "2022-03-01T14:43:13Z")
Now I have a DcmDataSet of dcmtk in my PC memory; I want to convert it to ITK image Data but not by reading a “.dcm” file. --- ## [ITK ERROR: Hematoxylin and Eosin are getting mixed up; failed](https://discourse.itk.org/t/itk-error-hematoxylin-and-eosin-are-getting-mixed-up-failed/4767)
**Author:** [@Jon](https://discourse.itk.org/u/Jon)\ **Replies:** 37\ **Last updated:** [March 1, 2022, 9:59am UTC](https://discourse.itk.org/t/itk-error-hematoxylin-and-eosin-are-getting-mixed-up-failed/4767 "2022-03-01T09:59:56Z")
I’m trying to help my doctor daughter by using machine learning to find tumors in her osteosarcoma histology slides. The H&E staining is poor — quite low but visible to humans – compared to that of the public domain data… --- ## [RegionOfInterestImageFilter to extract image slice from volume](https://discourse.itk.org/t/regionofinterestimagefilter-to-extract-image-slice-from-volume/4787)
**Author:** [@SofiaCV](https://discourse.itk.org/u/SofiaCV)\ **Replies:** 13\ **Last updated:** [February 28, 2022, 10:34am UTC](https://discourse.itk.org/t/regionofinterestimagefilter-to-extract-image-slice-from-volume/4787 "2022-02-28T10:34:20Z")
Hello, I’d like to extract a 2D slice from a MRI NIfTI file. I believe the RegionOfInterestImageFilter function in itk will do the job: https://itk.org/ITKExamples/src/Filtering/ImageGrid/ExtractRegionOfInterestInOneIm… --- ## [Is there any difference in performance (in Registration) between python and CSharp in SimpleITK?](https://discourse.itk.org/t/is-there-any-difference-in-performance-in-registration-between-python-and-csharp-in-simpleitk/4831)
**Author:** [@jpad](https://discourse.itk.org/u/jpad)\ **Replies:** 1\ **Last updated:** [February 27, 2022, 8:16pm UTC](https://discourse.itk.org/t/is-there-any-difference-in-performance-in-registration-between-python-and-csharp-in-simpleitk/4831 "2022-02-27T20:16:45Z")
I use version 2.2 of simpleitk. It was implemented by referring to the following code for registration. https://simpleitk.readthedocs.io/en/master/link\_ImageRegistrationMethodBSpline2\_docs.html Previously, image regis… --- ## [Compilation error after ITK-5.3 update](https://discourse.itk.org/t/compilation-error-after-itk-5-3-update/4832)
**Author:** [@Mik](https://discourse.itk.org/u/Mik)\ **Replies:** 3\ **Last updated:** [February 25, 2022, 7:41pm UTC](https://discourse.itk.org/t/compilation-error-after-itk-5-3-update/4832 "2022-02-25T19:41:25Z")
Dear developers, I have a problem with compilation of Plastimatch software. This program is a part of SlicerRT extension of 3D Slicer. Plastimatch build is failed after ITK-5.3 upgrade on Linux. CDash shows that Window… --- ## [how to balance the illumination( Correction of Intensity Inhomogeneity) in itk Montage](https://discourse.itk.org/t/how-to-balance-the-illumination-correction-of-intensity-inhomogeneity-in-itk-montage/4811)
**Author:** [@allen](https://discourse.itk.org/u/allen)\ **Replies:** 17\ **Last updated:** [February 25, 2022, 2:27pm UTC](https://discourse.itk.org/t/how-to-balance-the-illumination-correction-of-intensity-inhomogeneity-in-itk-montage/4811 "2022-02-25T14:27:00Z")
hello, i use itk stitch microscope tiles to whole slide image, it works really good, yet there are some grid shadow in the blending area like this i looked into it, it’s caused by the uneven illumination, this article … --- ## [Rotation Around a Specified Axis](https://discourse.itk.org/t/rotation-around-a-specified-axis/1875)
**Author:** [@DrJessop](https://discourse.itk.org/u/DrJessop)\ **Replies:** 9\ **Last updated:** [February 24, 2022, 1:43pm UTC](https://discourse.itk.org/t/rotation-around-a-specified-axis/1875 "2022-02-24T13:43:43Z")
I am trying to rotate an MRI image around the z-axis by 90 degrees. I can specify the center of rotation using an Euler3DTransform, however I cannot specify the direction of rotation (the image is diagonally rotated). Ho… --- ## [Maintenance today](https://discourse.itk.org/t/maintenance-today/4738)
**Author:** [@dzenanz](https://discourse.itk.org/u/dzenanz)\ **Replies:** 7\ **Last updated:** [February 24, 2022, 1:27pm UTC](https://discourse.itk.org/t/maintenance-today/4738 "2022-02-24T13:27:05Z")
We will move itk.org off of the old 32-bit Debian 10 server (public.kitware.com) to our updated 64-bit Ubuntu 20.04 server (web.kitware.com) today at 2pm (approximately 3.5h from now). The upgrade is likely to take up to… --- ## [ITK Install issues on VS2022](https://discourse.itk.org/t/itk-install-issues-on-vs2022/4821)
**Author:** [@xyz](https://discourse.itk.org/u/xyz)\ **Replies:** 13\ **Last updated:** [February 24, 2022, 9:43am UTC](https://discourse.itk.org/t/itk-install-issues-on-vs2022/4821 "2022-02-24T09:43:28Z")
Dear all, I was trying to install ITK for transforming the .TRE files from ITKTubeTK - Bullitt - Healthy MR Database to common image format for phantom for several days. My environment is python 3.10, ITK 5.2.1/ITK 5.3r… --- ## [Can I get the index of a point in a point container?](https://discourse.itk.org/t/can-i-get-the-index-of-a-point-in-a-point-container/4828)
**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\ **Replies:** 1\ **Last updated:** [February 23, 2022, 3:47pm UTC](https://discourse.itk.org/t/can-i-get-the-index-of-a-point-in-a-point-container/4828 "2022-02-23T15:47:29Z")
Can I get the index of a point in a point container? --- ## [Odd behavior with Numpy Array Views](https://discourse.itk.org/t/odd-behavior-with-numpy-array-views/4827)
**Author:** [@brandonfosso](https://discourse.itk.org/u/brandonfosso)\ **Replies:** 2\ **Last updated:** [February 23, 2022, 1:31am UTC](https://discourse.itk.org/t/odd-behavior-with-numpy-array-views/4827 "2022-02-23T01:31:21Z")
Hello, I was just experimenting with SimpleITK in a Jupyter Notebook and was surprised by the following behavior. \> junk = np.zeros((3,3), dtype=np.uint8) \> junk array(\[\[0, 0, 0\], \[0, 0, 0\], \[0, 0, 0\]\], dt… --- ## [Introducing VoxLogicA -- a declarative language and interpreter for image analysis using ITK, based on "spatial model checking"](https://discourse.itk.org/t/introducing-voxlogica-a-declarative-language-and-interpreter-for-image-analysis-using-itk-based-on-spatial-model-checking/1627)
**Author:** [@vincenzoml](https://discourse.itk.org/u/vincenzoml)\ **Replies:** 2\ **Last updated:** [February 22, 2022, 1:20pm UTC](https://discourse.itk.org/t/introducing-voxlogica-a-declarative-language-and-interpreter-for-image-analysis-using-itk-based-on-spatial-model-checking/1627 "2022-02-22T13:20:53Z")
Hi all, I’m new to the forum, I’m here to introduce a new project, ask a question related to a possible bug in SimpleITK, and beg for some support :slight\_smile: The VoxLogicA project At the ISTI-CNR in Pisa (Italy) … --- ## [Remove JAVA, RUBY, TCL, EXPLICIT wrapping targets](https://discourse.itk.org/t/remove-java-ruby-tcl-explicit-wrapping-targets/4818)
**Author:** [@hjmjohnson](https://discourse.itk.org/u/hjmjohnson)\ **Replies:** 1\ **Last updated:** [February 21, 2022, 3:06pm UTC](https://discourse.itk.org/t/remove-java-ruby-tcl-explicit-wrapping-targets/4818 "2022-02-21T15:06:40Z")
I would like to propose removing the defunct build capabilities of JAVA, RUBY, TCL, & EXPLICIT options. These build configurations are not supported or working for a long time. The removal of these packages allows to g… --- ## [nifti to dicom conversion introduces negative intensities](https://discourse.itk.org/t/nifti-to-dicom-conversion-introduces-negative-intensities/4798)
**Author:** [@Keyn34](https://discourse.itk.org/u/Keyn34)\ **Replies:** 23\ **Last updated:** [February 20, 2022, 5:06pm UTC](https://discourse.itk.org/t/nifti-to-dicom-conversion-introduces-negative-intensities/4798 "2022-02-20T17:06:56Z")
Hello everyone! When I try to convert a nifti file to a dicom series with ImageSeriesWriter, I encounter weird behavior when inspecting the results with ITK-SNAP. For a few cases the intensity range shifts from only pos… --- ## [Compiling ~MinimalPathExtraction~ with ITK 5.2.1](https://discourse.itk.org/t/compiling-minimalpathextraction-with-itk-5-2-1/4784)
**Author:** [@edgar](https://discourse.itk.org/u/edgar)\ **Replies:** 21\ **Last updated:** [February 19, 2022, 8:33pm UTC](https://discourse.itk.org/t/compiling-minimalpathextraction-with-itk-5-2-1/4784 "2022-02-19T20:33:33Z")
Hi! I am trying to build ITK with MinimalPathExtraction, because I want to try TubeTK. I am getting a compilation error. I would appreciate if we can keep my compilation flags, so that the compilation does not restart … --- ## [ImageSeriesReader read DICOM series with wrong order](https://discourse.itk.org/t/imageseriesreader-read-dicom-series-with-wrong-order/4813)
**Author:** [@hubutui](https://discourse.itk.org/u/hubutui)\ **Replies:** 7\ **Last updated:** [February 19, 2022, 2:05am UTC](https://discourse.itk.org/t/imageseriesreader-read-dicom-series-with-wrong-order/4813 "2022-02-19T02:05:09Z")
I read DICOM series according to this guide import SimpleITK as sitk reader = sitk.ImageSeriesReader() reader.SetFileNames(reader.GetGDCMSeriesFileNames("patient01")) img2 = reader.Execute() data2 = sitk.GetArrayFromIma… --- ## [How should I write a function that takes two images as inputs?](https://discourse.itk.org/t/how-should-i-write-a-function-that-takes-two-images-as-inputs/4812)
**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\ **Replies:** 1\ **Last updated:** [February 18, 2022, 2:34pm UTC](https://discourse.itk.org/t/how-should-i-write-a-function-that-takes-two-images-as-inputs/4812 "2022-02-18T14:34:39Z")
Can I write a function that takes two images as inputs and calculates the min pixel this way? I am following the deepcopy example. Thanks template \ void Min\_of\_Image(typename TImage::Pointer input, type… --- ## [Registration with a Versor with Python and without SimpleITK](https://discourse.itk.org/t/registration-with-a-versor-with-python-and-without-simpleitk/4806)
**Author:** [@edgar](https://discourse.itk.org/u/edgar)\ **Replies:** 12\ **Last updated:** [February 18, 2022, 2:07am UTC](https://discourse.itk.org/t/registration-with-a-versor-with-python-and-without-simpleitk/4806 "2022-02-18T02:07:56Z")
Continuing the discussion from 3D image registration with Python and without SimpleITK: Hello! Instead of the translation registration, I am now trying a registration with a versor. How can I do that? This is my code (… --- ## [how to use image streaming to reduce memory usage and cpu usage in image stitching](https://discourse.itk.org/t/how-to-use-image-streaming-to-reduce-memory-usage-and-cpu-usage-in-image-stitching/4795)
**Author:** [@allen](https://discourse.itk.org/u/allen)\ **Replies:** 10\ **Last updated:** [February 17, 2022, 2:52pm UTC](https://discourse.itk.org/t/how-to-use-image-streaming-to-reduce-memory-usage-and-cpu-usage-in-image-stitching/4795 "2022-02-17T14:52:15Z")
The cpu usage and memory usage is pretty high when stitching tiles into a single one. 140 tiles(2592\*1944) stitching occupy nearly 100% cpu usage for more than 60s. i wonder if the usage won’t be so high in the image st… --- ## [How to render DSA type DICOM file using JavaScript](https://discourse.itk.org/t/how-to-render-dsa-type-dicom-file-using-javascript/4809)
**Author:** [@sujaly](https://discourse.itk.org/u/sujaly)\ **Replies:** 3\ **Last updated:** [February 17, 2022, 4:20am UTC](https://discourse.itk.org/t/how-to-render-dsa-type-dicom-file-using-javascript/4809 "2022-02-17T04:20:53Z")
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