# Latest

**URL:** https://discourse.itk.org/latest.md?page=21

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

**Page:** 22

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## [MetaImage: M\_ReadElementsROI: data not read completely](https://discourse.itk.org/t/metaimage-m-readelementsroi-data-not-read-completely/4269)

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**Author:** [@JK\_Kim](https://discourse.itk.org/u/JK_Kim)\
**Replies:** 11\
**Last updated:** [July 22, 2023, 1:23pm UTC](https://discourse.itk.org/t/metaimage-m-readelementsroi-data-not-read-completely/4269 "2023-07-22T13:23:01Z")

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Hi I am using SimpleITK 2.0.2 and Python 3.7.9 to read a 3D CT image in the compressed mhd format (ct.mhd, ct.zraw). When I run the code below, I am getting the following message. “data not read completely”. So, I save…

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## [How to get auto WLWW with SImpleITK in JAVA](https://discourse.itk.org/t/how-to-get-auto-wlww-with-simpleitk-in-java/6085)

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**Author:** [@Salu\_Ramos](https://discourse.itk.org/u/Salu_Ramos)\
**Replies:** 1\
**Last updated:** [July 21, 2023, 7:36pm UTC](https://discourse.itk.org/t/how-to-get-auto-wlww-with-simpleitk-in-java/6085 "2023-07-21T19:36:39Z")

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For example, Radiant dicom viewer has “auto window level window width” preset marked as default, that is different for each dicom file. opening dicom file 1: opening dicom file 2: opening dicom file 3: The ques…

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## [Java SimpleITK Slice extraction and display with JavaFX](https://discourse.itk.org/t/java-simpleitk-slice-extraction-and-display-with-javafx/6055)

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**Author:** [@Salu\_Ramos](https://discourse.itk.org/u/Salu_Ramos)\
**Replies:** 18\
**Last updated:** [July 20, 2023, 5:48pm UTC](https://discourse.itk.org/t/java-simpleitk-slice-extraction-and-display-with-javafx/6055 "2023-07-20T17:48:21Z")

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Hi, i am trying to get a slice from any axis like axial, sagital or coronal from dicom volume, i already made it with python, but due to python limitations i migrate to java. this is how i load the volume: public sta…

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## [RuntimeError with number of expected elements for DisplacementFieldTransform](https://discourse.itk.org/t/runtimeerror-with-number-of-expected-elements-for-displacementfieldtransform/6076)

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**Author:** [@rtlim](https://discourse.itk.org/u/rtlim)\
**Replies:** 1\
**Last updated:** [July 18, 2023, 5:54pm UTC](https://discourse.itk.org/t/runtimeerror-with-number-of-expected-elements-for-displacementfieldtransform/6076 "2023-07-18T17:54:48Z")

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I’m trying to create a DisplacementFieldTransform using a MetaImage that I’ve saved, but I’m getting a runtime error and I haven’t found anything online related to it. This is what the error says: RuntimeError: Exceptio…

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## [NCI Imaging Data Commons July 2023 release announcement](https://discourse.itk.org/t/nci-imaging-data-commons-july-2023-release-announcement/6074)

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**Author:** [@fedorov](https://discourse.itk.org/u/fedorov)\
**Replies:** 0\
**Last updated:** [July 17, 2023, 9:35pm UTC](https://discourse.itk.org/t/nci-imaging-data-commons-july-2023-release-announcement/6074 "2023-07-17T21:35:29Z")

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Imaging Data Commons release v15 brings you Visible Human Dataset among several new collections, along with the improvements to the portal to simplify download process and new tutorials. See the details in the release an…

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## [How to initialize CenteredTransformInitializer for 3D-3D image registration for exhaustive search optimizer](https://discourse.itk.org/t/how-to-initialize-centeredtransforminitializer-for-3d-3d-image-registration-for-exhaustive-search-optimizer/6054)

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**Author:** [@thanuja](https://discourse.itk.org/u/thanuja)\
**Replies:** 2\
**Last updated:** [July 15, 2023, 2:25am UTC](https://discourse.itk.org/t/how-to-initialize-centeredtransforminitializer-for-3d-3d-image-registration-for-exhaustive-search-optimizer/6054 "2023-07-15T02:25:11Z")

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Hi All, I’m following the 2D image registration example(python) for exhaustive search optimizer: https://examples.itk.org/src/numerics/optimizers/exhaustiveoptimizer/documentation I want to do the same for 3D-3D image …

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## [How to get Metadata with SimpleITK in Java](https://discourse.itk.org/t/how-to-get-metadata-with-simpleitk-in-java/6066)

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**Author:** [@Salu\_Ramos](https://discourse.itk.org/u/Salu_Ramos)\
**Replies:** 2\
**Last updated:** [July 13, 2023, 6:34pm UTC](https://discourse.itk.org/t/how-to-get-metadata-with-simpleitk-in-java/6066 "2023-07-13T18:34:56Z")

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i have a dicom folder that contains many dicom files, i load then using this code: public static org.itk.simple.Image loadLocalFolder (Stage stage) throws Exception { String dicomFolderPath = LocalLoader.selectF…

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## [Using CMake for Configuring and Building ITK vs Using the Python Wrapper for journal paper ITK code.](https://discourse.itk.org/t/using-cmake-for-configuring-and-building-itk-vs-using-the-python-wrapper-for-journal-paper-itk-code/6061)

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**Author:** [@jzhangaps](https://discourse.itk.org/u/jzhangaps)\
**Replies:** 2\
**Last updated:** [July 12, 2023, 1:28pm UTC](https://discourse.itk.org/t/using-cmake-for-configuring-and-building-itk-vs-using-the-python-wrapper-for-journal-paper-itk-code/6061 "2023-07-12T13:28:51Z")

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Hi ITK discussion forum! I’m new to ITK and am going through the ITK software guide in order to be able to try this code: https://github.com/midas-journal/midas-journal-154/tree/master/DiffeomorphicDemons-2009-06-Vercau…

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## [ransform parameters' gradient method of normalised cross-correlation](https://discourse.itk.org/t/ransform-parameters-gradient-method-of-normalised-cross-correlation/6063)

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**Author:** [@baolin](https://discourse.itk.org/u/baolin)\
**Replies:** 0\
**Last updated:** [July 12, 2023, 1:04pm UTC](https://discourse.itk.org/t/ransform-parameters-gradient-method-of-normalised-cross-correlation/6063 "2023-07-12T13:04:08Z")

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I found calculation transform parameters’ gradient method of normalised cross-correlation in itkNormalizedCorrelationImageToImageMetric.hxx I don’t know why we calculate derivatives like this. I need you help to give m…

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## [slice along a random direction to get 2D slice from 3D volume](https://discourse.itk.org/t/slice-along-a-random-direction-to-get-2d-slice-from-3d-volume/6056)

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**Author:** [@swetha.bsharma](https://discourse.itk.org/u/swetha.bsharma)\
**Replies:** 0\
**Last updated:** [July 11, 2023, 3:59pm UTC](https://discourse.itk.org/t/slice-along-a-random-direction-to-get-2d-slice-from-3d-volume/6056 "2023-07-11T15:59:34Z")

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Hi, I want to reslice a volume in a user defined direction. I have used LookatTransform in c++ version long time back ,I am not able to find it in the python version.Is there a similar transform available in python. i…

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## [Unable to perform simple image registration](https://discourse.itk.org/t/unable-to-perform-simple-image-registration/6053)

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**Author:** [@sarthakpati](https://discourse.itk.org/u/sarthakpati)\
**Replies:** 1\
**Last updated:** [July 11, 2023, 2:48pm UTC](https://discourse.itk.org/t/unable-to-perform-simple-image-registration/6053 "2023-07-11T14:48:12Z")

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Hi, Duplicate of Unable to perform simple image registration · Issue #1956 · SimpleITK/SimpleITK · GitHub, as I was directed to ask the question here. I am using SimpleITK-SimpleElastix since SimpleITK-2.2.1 seem to gi…

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## [Implementation of a Custom ImageToImage Similarity Metric for Registration](https://discourse.itk.org/t/implementation-of-a-custom-imagetoimage-similarity-metric-for-registration/6047)

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**Author:** [@JRopers](https://discourse.itk.org/u/JRopers)\
**Replies:** 5\
**Last updated:** [July 10, 2023, 3:07pm UTC](https://discourse.itk.org/t/implementation-of-a-custom-imagetoimage-similarity-metric-for-registration/6047 "2023-07-10T15:07:35Z")

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Hello ITK community! I am in desperate need for help as I am finding no resources on this. I am trying to implement a custom ImageToImage similarity metric for the purpose of registration. For a project, I want to regis…

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## [SimpleITK 2.3 Release Candidate 1](https://discourse.itk.org/t/simpleitk-2-3-release-candidate-1/6050)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 0\
**Last updated:** [July 10, 2023, 3:04pm UTC](https://discourse.itk.org/t/simpleitk-2-3-release-candidate-1/6050 "2023-07-10T15:04:41Z")

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Announcement Announcing the SimpleITK 2.3 Release Candidate 1! Users and developers are encouraged to test the RC before the final release and report issues, bugs, and any compatibility problems. Installing SimpleITK C…

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## [How can I find coordinates of a point after resampling?](https://discourse.itk.org/t/how-can-i-find-coordinates-of-a-point-after-resampling/6046)

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**Author:** [@Eloy\_Schultz](https://discourse.itk.org/u/Eloy_Schultz)\
**Replies:** 2\
**Last updated:** [July 10, 2023, 11:52am UTC](https://discourse.itk.org/t/how-can-i-find-coordinates-of-a-point-after-resampling/6046 "2023-07-10T11:52:42Z")

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Suppose I apply a resampling operation to my image as below: resampler = sitk.ResampleImageFilter() resampler.SetSize(target\_size) resampler.SetOutputSpacing(target\_spacing) resampler.SetOutputOrigin(ori…

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## [Java Convert int\[\] to VectorUInt32](https://discourse.itk.org/t/java-convert-int-to-vectoruint32/6037)

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**Author:** [@Salu\_Ramos](https://discourse.itk.org/u/Salu_Ramos)\
**Replies:** 9\
**Last updated:** [July 7, 2023, 10:17pm UTC](https://discourse.itk.org/t/java-convert-int-to-vectoruint32/6037 "2023-07-07T22:17:55Z")

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The SImpleITK.extract method requires 3 parameters: first is org.itk.simple.Image second is org.itk.simple.VectorUInt32 third is org.itk.simple.VectorInt32 i know whats are this parameters, i was able to reproduce this…

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## [itk::fem updating displacements](https://discourse.itk.org/t/itk-fem-updating-displacements/404)

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**Author:** [@nasil122002](https://discourse.itk.org/u/nasil122002)\
**Replies:** 0\
**Last updated:** [November 9, 2017, 7:55pm UTC](https://discourse.itk.org/t/itk-fem-updating-displacements/404 "2017-11-09T19:55:56Z")

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Dear ITK users, I have another question. In order to visualize the deformation, I want to replace the old node coordinates with the new one after generating the solution, like in UpdateDisplacements() function in itkFe…

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## [Convert TIFF to ITK](https://discourse.itk.org/t/convert-tiff-to-itk/6040)

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**Author:** [@itkusers](https://discourse.itk.org/u/itkusers)\
**Replies:** 1\
**Last updated:** [July 6, 2023, 7:16pm UTC](https://discourse.itk.org/t/convert-tiff-to-itk/6040 "2023-07-06T19:16:33Z")

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Hi everyone: My lab group is interested in using ITK-compatible files for the image segmentation platform VesSAP: GitHub - vessap/vessap: Experimental code and examples for: Automated analysis of whole brain vasculature…

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## [Csharp \[c#\] wrappings for ITK (and Plastimatch)](https://discourse.itk.org/t/csharp-c-wrappings-for-itk-and-plastimatch/5472)

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**Author:** [@G\_Tom](https://discourse.itk.org/u/G_Tom)\
**Replies:** 5\
**Last updated:** [July 5, 2023, 8:51pm UTC](https://discourse.itk.org/t/csharp-c-wrappings-for-itk-and-plastimatch/5472 "2023-07-05T20:51:08Z")

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Hi , I want to use itk from C# application. So far, I know simple itk works with c# but I am interested in using the plastimatch library which is simply heavily built on ITK. Plastimatch documentation — Plastimatch 1.9.…

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## [Republish figure from ITK Software Guide?](https://discourse.itk.org/t/republish-figure-from-itk-software-guide/6036)

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**Author:** [@gcsharp](https://discourse.itk.org/u/gcsharp)\
**Replies:** 2\
**Last updated:** [July 5, 2023, 8:40pm UTC](https://discourse.itk.org/t/republish-figure-from-itk-software-guide/6036 "2023-07-05T20:40:28Z")

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Hello and good morning! I am co-author on a review article that summarizes guidelines for the use of image registration in radiation therapy. We would like to include the famous ITK generic registration (v3) workflow f…

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## [Random access to image data](https://discourse.itk.org/t/random-access-to-image-data/6034)

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**Author:** [@cookpa](https://discourse.itk.org/u/cookpa)\
**Replies:** 2\
**Last updated:** [July 5, 2023, 4:53pm UTC](https://discourse.itk.org/t/random-access-to-image-data/6034 "2023-07-05T16:53:49Z")

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Hi all, Is there support in ITK for random access to image data? Specifically, I’m trying to figure out if it’s possible to read in a single input volume from a 4D time series, without reading the entire 4D array from …

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## [Error message may need rephrasing](https://discourse.itk.org/t/error-message-may-need-rephrasing/5814)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 2\
**Last updated:** [July 5, 2023, 12:19am UTC](https://discourse.itk.org/t/error-message-may-need-rephrasing/5814 "2023-07-05T00:19:59Z")

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Hi! I found that doing this: DisplacementFieldNumpy = np.ones( (3, 4, 100, 100)) PyBuffer = itk.PyBuffer\[VectorImageType\] DisplacementField = PyBuffer.GetImageFromArray(DisplacementFieldNumpy) yields RuntimeError:…

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## [VTK to simpleITK conversion in Python](https://discourse.itk.org/t/vtk-to-simpleitk-conversion-in-python/4028)

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**Author:** [@Andrea\_Borsic](https://discourse.itk.org/u/Andrea_Borsic)\
**Replies:** 6\
**Last updated:** [July 3, 2023, 8:35pm UTC](https://discourse.itk.org/t/vtk-to-simpleitk-conversion-in-python/4028 "2023-07-03T20:35:23Z")

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Hello All, Does anyone has any tip or code snippet for converting a vtk image to simpleITK and vice-versa in memory using python? Thanks in advance for any tip / advice. Best Regards, Andrea

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## [Slice 3D volume along a specific axis using python ITK](https://discourse.itk.org/t/slice-3d-volume-along-a-specific-axis-using-python-itk/6005)

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**Author:** [@zemmyang](https://discourse.itk.org/u/zemmyang)\
**Replies:** 7\
**Last updated:** [June 29, 2023, 2:00pm UTC](https://discourse.itk.org/t/slice-3d-volume-along-a-specific-axis-using-python-itk/6005 "2023-06-29T14:00:41Z")

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I found Read DICOM Series and Write 3D Image — v5.3.0 and it works, but I can only get slices from one axis (along z in my case). Is there a way to specify which axis I’m slicing along (I need x and y as well). I saw a …

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## [Call for Papers - MICCAI'23 Third Workshop on Shape Analysis in Medical Imaging (SHAPEMI)](https://discourse.itk.org/t/call-for-papers-miccai23-third-workshop-on-shape-analysis-in-medical-imaging-shapemi/5959)

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**Author:** [@bpaniagua](https://discourse.itk.org/u/bpaniagua)\
**Replies:** 1\
**Last updated:** [June 27, 2023, 5:16pm UTC](https://discourse.itk.org/t/call-for-papers-miccai23-third-workshop-on-shape-analysis-in-medical-imaging-shapemi/5959 "2023-06-27T17:16:51Z")

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Dear all, I would like to bring to your attention the third “Shape in Medical Imaging (ShapeMI)” workshop, which is to be held in conjunction with the MICCAI 2023 conference. Best regards, Bea MICCAI SHAPEMI Worksh…

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## [Registration with ITK not working - Unexplainable Erros](https://discourse.itk.org/t/registration-with-itk-not-working-unexplainable-erros/6021)

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**Author:** [@JRopers](https://discourse.itk.org/u/JRopers)\
**Replies:** 2\
**Last updated:** [June 27, 2023, 8:40am UTC](https://discourse.itk.org/t/registration-with-itk-not-working-unexplainable-erros/6021 "2023-06-27T08:40:38Z")

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Hello everyone! I have come here as a last resort as I am really struggling to get ITK to run. First of all, some information on my system: OS: Windows 11 Visual Studio: 2017 Architecture: x64 C++ Standard: v141 No…

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## [Resampling volume to axial view with SimpleITK](https://discourse.itk.org/t/resampling-volume-to-axial-view-with-simpleitk/6010)

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**Author:** [@mortifiedpenguin](https://discourse.itk.org/u/mortifiedpenguin)\
**Replies:** 2\
**Last updated:** [June 26, 2023, 12:38pm UTC](https://discourse.itk.org/t/resampling-volume-to-axial-view-with-simpleitk/6010 "2023-06-26T12:38:24Z")

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Hi all, I want to resample medical volume datasets such that they are always oriented axial. I’ve managed to get it to work more or less using the following code (C# but should be clear enough:) Image l…

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## [Hurry! Some problems about similarity measurement.](https://discourse.itk.org/t/hurry-some-problems-about-similarity-measurement/6011)

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**Author:** [@ljjiayou](https://discourse.itk.org/u/ljjiayou)\
**Replies:** 6\
**Last updated:** [June 25, 2023, 7:12am UTC](https://discourse.itk.org/t/hurry-some-problems-about-similarity-measurement/6011 "2023-06-25T07:12:09Z")

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I am doing a task, which is to rotate the reference image and the registered image to observe the change of the evaluation index. Is there any relevant code? I also need to observe different evaluation indicators. What …

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## [Transformation matrix](https://discourse.itk.org/t/transformation-matrix/6004)

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**Author:** [@feeling](https://discourse.itk.org/u/feeling)\
**Replies:** 3\
**Last updated:** [June 25, 2023, 1:57am UTC](https://discourse.itk.org/t/transformation-matrix/6004 "2023-06-25T01:57:05Z")

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Hello everyone: I am using SimpleITK to align a set of images, let’s say A is a fixed image and B is a moving image, I have done various alignments including Translation, Euler, Affine and got a series of TransformParam…

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## [Powell optimizer cannot work properly](https://discourse.itk.org/t/powell-optimizer-cannot-work-properly/6014)

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**Author:** [@suzume](https://discourse.itk.org/u/suzume)\
**Replies:** 0\
**Last updated:** [June 24, 2023, 8:48am UTC](https://discourse.itk.org/t/powell-optimizer-cannot-work-properly/6014 "2023-06-24T08:48:18Z")

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Hi, I want to use the PowellOptimizer as the optimizer in registration. However, when I use PowellOptimizer, the registration cannot start and it stuck at the beginning as shown below: It always staying the “Starting…

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## [Can't get right DRR](https://discourse.itk.org/t/cant-get-right-drr/6007)

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**Author:** [@suzume](https://discourse.itk.org/u/suzume)\
**Replies:** 4\
**Last updated:** [June 22, 2023, 3:38pm UTC](https://discourse.itk.org/t/cant-get-right-drr/6007 "2023-06-22T15:38:15Z")

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Hi, I was using GetDRRSiddonJacobsRayTracing.cxx to generate DRR images. However I can’t generate the right DRR images as the images generated by the author. The parameters are set as the author proposed, which are -rp …

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