# Latest

**URL:** https://discourse.itk.org/latest.md?page=17

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

**Page:** 18

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## [Simple ITK with Elastix has earlier version of N4BiasFieldCorrectionImageFilter](https://discourse.itk.org/t/simple-itk-with-elastix-has-earlier-version-of-n4biasfieldcorrectionimagefilter/6336)

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**Author:** [@J\_B](https://discourse.itk.org/u/J_B)\
**Replies:** 2\
**Last updated:** [December 4, 2023, 2:00pm UTC](https://discourse.itk.org/t/simple-itk-with-elastix-has-earlier-version-of-n4biasfieldcorrectionimagefilter/6336 "2023-12-04T14:00:54Z")

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Hello, I have used SimpleITK.N4BiasFieldCorrectionImageFilter() successfully, and SimpleITK.ElastixImageFilter() successfully to do a registration, but when SimpleITK-SimpleElastix is pip installed into a python virtual …

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## [Error Compiling ITK 5.3.0](https://discourse.itk.org/t/error-compiling-itk-5-3-0/6333)

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**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 5\
**Last updated:** [December 2, 2023, 6:37pm UTC](https://discourse.itk.org/t/error-compiling-itk-5-3-0/6333 "2023-12-02T18:37:54Z")

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We have some C++ software that was compiling fine against ITK 5.2.1. In an effort to get up to date I am trying to compile against ITK 5.3.0 using Visual Studio 17 2022. I am getting the following compile error. FAILED:…

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## [how to determine the orientation of a two-dimensional Image?](https://discourse.itk.org/t/how-to-determine-the-orientation-of-a-two-dimensional-image/6329)

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**Author:** [@Salu\_Ramos](https://discourse.itk.org/u/Salu_Ramos)\
**Replies:** 0\
**Last updated:** [December 1, 2023, 6:05pm UTC](https://discourse.itk.org/t/how-to-determine-the-orientation-of-a-two-dimensional-image/6329 "2023-12-01T18:05:05Z")

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i’m using SimpleITK.extract(image, size\[\], index\[x\]) to extract a cross section from a series. And I need to determine the orientation of this cross section with: posterior, anterior, right, left, inferior and superior. …

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## [Reading dicom series with SimpleITK and filesort](https://discourse.itk.org/t/reading-dicom-series-with-simpleitk-and-filesort/1577)

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**Author:** [@jonasteuwen](https://discourse.itk.org/u/jonasteuwen)\
**Replies:** 8\
**Last updated:** [December 1, 2023, 2:27pm UTC](https://discourse.itk.org/t/reading-dicom-series-with-simpleitk-and-filesort/1577 "2023-12-01T14:27:20Z")

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I am trying to read DICOM series using SimpleITK. The current situation is that I have a folders with a lot of dicom series in there, and I only need a few. Luckily I know the prefix of the filenames so I can select the …

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## [Use JoinSeriesImageFilter to append 4D images into 5D](https://discourse.itk.org/t/use-joinseriesimagefilter-to-append-4d-images-into-5d/6324)

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**Author:** [@cpinter](https://discourse.itk.org/u/cpinter)\
**Replies:** 3\
**Last updated:** [November 30, 2023, 2:16pm UTC](https://discourse.itk.org/t/use-joinseriesimagefilter-to-append-4d-images-into-5d/6324 "2023-11-30T14:16:56Z")

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Hi all, I have a series of 4D images (3D + scalar component) with the same dimensions, scalar type, number of scalar components, and I’d like to append them into a single image (a time or other type of sequence of image…

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## [Checking simpleitk.Image Equality](https://discourse.itk.org/t/checking-simpleitk-image-equality/6323)

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**Author:** [@Franciska](https://discourse.itk.org/u/Franciska)\
**Replies:** 5\
**Last updated:** [November 29, 2023, 3:37pm UTC](https://discourse.itk.org/t/checking-simpleitk-image-equality/6323 "2023-11-29T15:37:19Z")

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Hi! I have two methods to the same task. I’d like to check, whether the result of the two methods gives equal outcomes. The files are nifti Images. I can check if their numpy part is the same easily: output1=sitk.Read…

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## [Build error with g++ 13.2](https://discourse.itk.org/t/build-error-with-g-13-2/6317)

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**Author:** [@codeling](https://discourse.itk.org/u/codeling)\
**Replies:** 3\
**Last updated:** [November 28, 2023, 7:34am UTC](https://discourse.itk.org/t/build-error-with-g-13-2/6317 "2023-11-28T07:34:53Z")

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Just tried building ITK 5.4rc1 with g++ 13.2.1 on Fedora 39 (I erroneously reported clang 17 before, which I thought the build was using, but the compiler didn’t get set properly, the build was actually running with g++)…

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## [ITK and Gpu processing](https://discourse.itk.org/t/itk-and-gpu-processing/6319)

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**Author:** [@Mahdiye\_Imanpanah](https://discourse.itk.org/u/Mahdiye_Imanpanah)\
**Replies:** 2\
**Last updated:** [November 27, 2023, 3:08pm UTC](https://discourse.itk.org/t/itk-and-gpu-processing/6319 "2023-11-27T15:08:13Z")

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Hello everyone. I use itk c++ and simpleitk c# for my projects. I see GPU-related questions in the forum of itk, but I can’t find the best way to use it. I can not see information about this in the ItkSoftwareGuid, Do…

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## [How to convert 4D fMRI images to a series of 3D images?](https://discourse.itk.org/t/how-to-convert-4d-fmri-images-to-a-series-of-3d-images/6322)

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**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 1\
**Last updated:** [November 27, 2023, 2:08pm UTC](https://discourse.itk.org/t/how-to-convert-4d-fmri-images-to-a-series-of-3d-images/6322 "2023-11-27T14:08:55Z")

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Hello, I am working with the ADHD200 dataset. It consists of anatomical and resting state fMRI images in NIFTI (nii.gz) format. The fMRI images are 4D images. These represent 3D image of the brain over a period of time…

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## [Is there a bug in InPlaceImageFilter?](https://discourse.itk.org/t/is-there-a-bug-in-inplaceimagefilter/6318)

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**Author:** [@mihail.isakov](https://discourse.itk.org/u/mihail.isakov)\
**Replies:** 1\
**Last updated:** [November 27, 2023, 1:02pm UTC](https://discourse.itk.org/t/is-there-a-bug-in-inplaceimagefilter/6318 "2023-11-27T13:02:55Z")

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I see this in SimpleITK’s Todo List The link points to ITK’s InPlaceImageFilter. Is there an issue or more information about the bug? Thanks!

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## [Combining overlapping segmentations of same region from different images.](https://discourse.itk.org/t/combining-overlapping-segmentations-of-same-region-from-different-images/6309)

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**Author:** [@ramirez](https://discourse.itk.org/u/ramirez)\
**Replies:** 11\
**Last updated:** [November 23, 2023, 3:04pm UTC](https://discourse.itk.org/t/combining-overlapping-segmentations-of-same-region-from-different-images/6309 "2023-11-23T15:04:19Z")

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Hello everyone, There is a certain region in these images (MRI) whose boundaries end in one view but can be easily observed in another ( e.g., the posterior limit in the coronal plane can be extended in the sagittal pla…

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## [Resolving Image Cropping Issue in NIFTI Image Resampling](https://discourse.itk.org/t/resolving-image-cropping-issue-in-nifti-image-resampling/6313)

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**Author:** [@hjy0404](https://discourse.itk.org/u/hjy0404)\
**Replies:** 3\
**Last updated:** [November 21, 2023, 3:05am UTC](https://discourse.itk.org/t/resolving-image-cropping-issue-in-nifti-image-resampling/6313 "2023-11-21T03:05:56Z")

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I am trying to resample a NIFTI image from a resolution of 512,512,661 to 512,512,147 using SimpleITK. Below is the code I’ve used: def resample\_to\_original\_size(isotropic\_img, ref\_img): original\_spacing = ref\_img.…

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## [N4BiasFieldCorrectionImageFilter: GetLogBiasFieldAsImage, wrap BSplineControlPointImageFilter, alternatives](https://discourse.itk.org/t/n4biasfieldcorrectionimagefilter-getlogbiasfieldasimage-wrap-bsplinecontrolpointimagefilter-alternatives/5142)

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**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 4\
**Last updated:** [November 20, 2023, 9:18pm UTC](https://discourse.itk.org/t/n4biasfieldcorrectionimagefilter-getlogbiasfieldasimage-wrap-bsplinecontrolpointimagefilter-alternatives/5142 "2023-11-20T21:18:15Z")

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With SimpleITK I can do: def bias\_correct( input: sitk.Image, mask: sitk.Image = None, shrink\_factor: int = 4, num\_fitting\_levels: int = 4, num\_iterations: int = 50, ) -\> sitk.Image: """Perform N…

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## [Registration mask and rigidity penalty](https://discourse.itk.org/t/registration-mask-and-rigidity-penalty/6311)

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**Author:** [@calici](https://discourse.itk.org/u/calici)\
**Replies:** 0\
**Last updated:** [November 20, 2023, 2:47am UTC](https://discourse.itk.org/t/registration-mask-and-rigidity-penalty/6311 "2023-11-20T02:47:36Z")

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My questions is actually the continuation of elastix group discussion.. Currently I am trying to assess treatment success by registering pretreatment CT and post treatment CT. I want to keep the lesion region undeformed…

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## [Use of TransformRigidityPenalty Fails](https://discourse.itk.org/t/use-of-transformrigiditypenalty-fails/6273)

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**Author:** [@calici](https://discourse.itk.org/u/calici)\
**Replies:** 2\
**Last updated:** [November 17, 2023, 1:51pm UTC](https://discourse.itk.org/t/use-of-transformrigiditypenalty-fails/6273 "2023-11-17T13:51:34Z")

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Hi! I am using deformable intensity-based algorithm to register pretreatment and posttreatment CT pairs. I want a specific region defined by a segmentation not to be deformed much during nonlinear registration. For tha…

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## [registration of simple matrices of point](https://discourse.itk.org/t/registration-of-simple-matrices-of-point/6303)

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**Author:** [@Fabrizio\_B](https://discourse.itk.org/u/Fabrizio_B)\
**Replies:** 3\
**Last updated:** [November 16, 2023, 1:43pm UTC](https://discourse.itk.org/t/registration-of-simple-matrices-of-point/6303 "2023-11-16T13:43:33Z")

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Hello everybody, in my project we work with medical images of biopsies. Upstream, they analyze such images and convert the important features in CSV format. I find myself then with big data frames, containing the posi…

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## [Multi-resolution registration](https://discourse.itk.org/t/multi-resolution-registration/6300)

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**Author:** [@maxtj](https://discourse.itk.org/u/maxtj)\
**Replies:** 1\
**Last updated:** [November 15, 2023, 2:11pm UTC](https://discourse.itk.org/t/multi-resolution-registration/6300 "2023-11-15T14:11:44Z")

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I am very new to python and the use of SimpleITK. I have tried to construct python code to register 2 image modalities that have different spatial resolutions. I could not perform registration between 2 images if one of …

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## [IntensityWindowingImageFilter not working as expected with multiframe instances (JAVA)](https://discourse.itk.org/t/intensitywindowingimagefilter-not-working-as-expected-with-multiframe-instances-java/6289)

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**Author:** [@Salu\_Ramos](https://discourse.itk.org/u/Salu_Ramos)\
**Replies:** 7\
**Last updated:** [November 14, 2023, 9:27pm UTC](https://discourse.itk.org/t/intensitywindowingimagefilter-not-working-as-expected-with-multiframe-instances-java/6289 "2023-11-14T21:27:52Z")

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i have recorded my problem: As you can see, weasis is clearly displaying the image with \[128, 256\] and my software shows everything in white with same configuration. This is the function that applys the f…

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## [How to use a deformationField to deform a new volume?](https://discourse.itk.org/t/how-to-use-a-deformationfield-to-deform-a-new-volume/6294)

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**Author:** [@PolarBean](https://discourse.itk.org/u/PolarBean)\
**Replies:** 0\
**Last updated:** [November 8, 2023, 8:11pm UTC](https://discourse.itk.org/t/how-to-use-a-deformationfield-to-deform-a-new-volume/6294 "2023-11-08T20:11:02Z")

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Hi, Thank you for working on this package. I am using GitHub - SuperElastix/SimpleElastix: Multi-lingual medical image registration library which has now been integrated into SimpleITK. I have generated a deformation f…

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## [Reading and extracting images from a large DICOM file](https://discourse.itk.org/t/reading-and-extracting-images-from-a-large-dicom-file/6292)

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**Author:** [@Viktor\_Ustynov](https://discourse.itk.org/u/Viktor_Ustynov)\
**Replies:** 6\
**Last updated:** [November 8, 2023, 6:00pm UTC](https://discourse.itk.org/t/reading-and-extracting-images-from-a-large-dicom-file/6292 "2023-11-08T18:00:16Z")

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Hi everyone, I’m a beginner with ITK. I need to extract all the images from a very large (about 3 GB) .dcm file and save them as .bmp files. To do this, I’m trying to read the file as shown in the examples. However, t…

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## [ITK Documentation Hackathon, November 2023!](https://discourse.itk.org/t/itk-documentation-hackathon-november-2023/6260)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 3\
**Last updated:** [November 8, 2023, 2:56pm UTC](https://discourse.itk.org/t/itk-documentation-hackathon-november-2023/6260 "2023-11-08T14:56:48Z")

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The Insight Toolkit (ITK) is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration. The ITK Documentation Hackathon aims to bring together ITK developers an…

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## [Dice score and Hausdorff distance for inter-modal image registration](https://discourse.itk.org/t/dice-score-and-hausdorff-distance-for-inter-modal-image-registration/6268)

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**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 9\
**Last updated:** [November 8, 2023, 12:03pm UTC](https://discourse.itk.org/t/dice-score-and-hausdorff-distance-for-inter-modal-image-registration/6268 "2023-11-08T12:03:42Z")

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I have 3D CT and MR images of the brain. I want to register these images and find out Dice score, Hausdorff distance, Jaccard index as measure of registration accuracy. I have segmented the whole brain (both CT and MR i…

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## [How to extract frame from Multiframe Image/FrameSet? (JAVA)](https://discourse.itk.org/t/how-to-extract-frame-from-multiframe-image-frameset-java/6288)

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**Author:** [@Salu\_Ramos](https://discourse.itk.org/u/Salu_Ramos)\
**Replies:** 4\
**Last updated:** [November 7, 2023, 7:34pm UTC](https://discourse.itk.org/t/how-to-extract-frame-from-multiframe-image-frameset-java/6288 "2023-11-07T19:34:23Z")

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I have a multiframe instance loaded with ImageSeriesReader, and i want to know how am i supposed to extract a frame from the result Image/frameSet. The below script was working fine for singleframe instances loaded as a…

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## [How to disable logging in python, jupyter notebook](https://discourse.itk.org/t/how-to-disable-logging-in-python-jupyter-notebook/6281)

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**Author:** [@hucang0](https://discourse.itk.org/u/hucang0)\
**Replies:** 4\
**Last updated:** [November 6, 2023, 3:52pm UTC](https://discourse.itk.org/t/how-to-disable-logging-in-python-jupyter-notebook/6281 "2023-11-06T15:52:44Z")

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I am executing parallel processes in VS Code on Ubuntu, with each process invoking SimpleITK. However, the console output from these processes is causing VS Code to crash. How can I disable the logging?

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## [Use BRAINSFit in a Python in-house software](https://discourse.itk.org/t/use-brainsfit-in-a-python-in-house-software/6283)

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**Author:** [@Icron1](https://discourse.itk.org/u/Icron1)\
**Replies:** 1\
**Last updated:** [November 6, 2023, 1:31pm UTC](https://discourse.itk.org/t/use-brainsfit-in-a-python-in-house-software/6283 "2023-11-06T13:31:33Z")

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Hello dear community, I am looking to use the BRAINSFit registration algorithm in a custom Python software to align cerebral MRIs. Is it possible to implement it in a Python-based software without using Slicer (which is…

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## [why can't itk read dicomdir files?](https://discourse.itk.org/t/why-cant-itk-read-dicomdir-files/6274)

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**Author:** [@zx-lhb](https://discourse.itk.org/u/zx-lhb)\
**Replies:** 3\
**Last updated:** [November 6, 2023, 2:54am UTC](https://discourse.itk.org/t/why-cant-itk-read-dicomdir-files/6274 "2023-11-06T02:54:00Z")

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hi, I tried to read dicom files which are all stored in a directory using the following code void readDicomSeries(const std::string& dicom\_dir, itk::Image\<float, 3\>::Pointer& out\_image) { using ImageIOType = itk::GD…

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## [Evaluation of the registered image](https://discourse.itk.org/t/evaluation-of-the-registered-image/6275)

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**Author:** [@pratibha](https://discourse.itk.org/u/pratibha)\
**Replies:** 4\
**Last updated:** [November 5, 2023, 7:48pm UTC](https://discourse.itk.org/t/evaluation-of-the-registered-image/6275 "2023-11-05T19:48:17Z")

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I want to evaluate whether the registration is done properly or not automatically or based on some metric. Normally I check it by manually aligning the registered image on the fixed image and for the TRE approach, I had …

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## [Error in plotting multi-slice images in SimpleITK (Jupyter Notebook)](https://discourse.itk.org/t/error-in-plotting-multi-slice-images-in-simpleitk-jupyter-notebook/6279)

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**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 1\
**Last updated:** [November 4, 2023, 3:59pm UTC](https://discourse.itk.org/t/error-in-plotting-multi-slice-images-in-simpleitk-jupyter-notebook/6279 "2023-11-04T15:59:09Z")

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I newly configured SimpleITK in my laptop. While test-running a few example codes, the following error is showing. This is happening only in case of images with multiple slices and the interactive images. I checked a…

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## [Reading Dicom sequence data with SimpleITK](https://discourse.itk.org/t/reading-dicom-sequence-data-with-simpleitk/2877)

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**Author:** [@jonasteuwen](https://discourse.itk.org/u/jonasteuwen)\
**Replies:** 14\
**Last updated:** [October 31, 2023, 7:41am UTC](https://discourse.itk.org/t/reading-dicom-sequence-data-with-simpleitk/2877 "2023-10-31T07:41:50Z")

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When reading mammography images there are several Dicom tags relevant to be able to display the image correctly as described in the dicom standard. These are stored in the VOILUTFunction and VOILUTSequence. The first is …

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## [N4 bias field correction - Can't find "spline spacing" in simpleITK](https://discourse.itk.org/t/n4-bias-field-correction-cant-find-spline-spacing-in-simpleitk/6267)

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**Author:** [@tonkeln](https://discourse.itk.org/u/tonkeln)\
**Replies:** 4\
**Last updated:** [October 30, 2023, 10:25am UTC](https://discourse.itk.org/t/n4-bias-field-correction-cant-find-spline-spacing-in-simpleitk/6267 "2023-10-30T10:25:40Z")

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Hello everyone, In 3D Slicer (and ANTs) there is the parameter “spline spacing” or “spline distance” to define the distance between control points for the N4 bias field correction. I would like to reproduce a paper whe…

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