# Latest

**URL:** https://discourse.itk.org/latest.md?page=14

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

**Page:** 15

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## [ITK Error](https://discourse.itk.org/t/itk-error/6521)

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**Author:** [@skb](https://discourse.itk.org/u/skb)\
**Replies:** 3\
**Last updated:** [March 20, 2024, 1:06am UTC](https://discourse.itk.org/t/itk-error/6521 "2024-03-20T01:06:25Z")

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itk::ExceptionObject (00000079F50FBB38) Location: “class itk::SmartPointer\<class itk::RealToHalfHermitianForwardFFTImageFilter\<class itk::Image\<float,3\>,class itk::Image\<class std::complex,3\> \> \> \_\_cdecl itk::RealToHalf…

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## [Setting an Initial Transform for Elastix](https://discourse.itk.org/t/setting-an-initial-transform-for-elastix/6532)

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**Author:** [@lschuring](https://discourse.itk.org/u/lschuring)\
**Replies:** 1\
**Last updated:** [March 19, 2024, 8:33pm UTC](https://discourse.itk.org/t/setting-an-initial-transform-for-elastix/6532 "2024-03-19T20:33:51Z")

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Hi ITK community! I am setting up a pipeline in python to register MRI image stacks which tend to have poor initial alignment. I would like to provide an elastix image filter (sitk.ElastixImageFilter()) an initial trans…

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## [Different include file paths between build-from-source and installed](https://discourse.itk.org/t/different-include-file-paths-between-build-from-source-and-installed/6531)

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**Author:** [@jilei-hao](https://discourse.itk.org/u/jilei-hao)\
**Replies:** 1\
**Last updated:** [March 19, 2024, 3:50pm UTC](https://discourse.itk.org/t/different-include-file-paths-between-build-from-source-and-installed/6531 "2024-03-19T15:50:21Z")

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Hi, I’m working on upgrading our projects references to itk5.4. When I changed itk reference from a build-from-source directory to an installed directory, some of the #include no longer work. Here are two examples: // …

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## [Convert a displacement filed nifty image to SITK transform type](https://discourse.itk.org/t/convert-a-displacement-filed-nifty-image-to-sitk-transform-type/4210)

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**Author:** [@VHK](https://discourse.itk.org/u/VHK)\
**Replies:** 4\
**Last updated:** [March 19, 2024, 12:53pm UTC](https://discourse.itk.org/t/convert-a-displacement-filed-nifty-image-to-sitk-transform-type/4210 "2024-03-19T12:53:40Z")

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Hello everyone, I have a displacement field Nifti format (field.nii.gz). How can I convert it to sitk.transform type (field.tfm) so that I can use it as transformation in SITK? I really appreciate any help you can prov…

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## [Issue with the RTK output generated using a head phantom](https://discourse.itk.org/t/issue-with-the-rtk-output-generated-using-a-head-phantom/6520)

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**Author:** [@Navami\_123](https://discourse.itk.org/u/Navami_123)\
**Replies:** 9\
**Last updated:** [March 19, 2024, 12:15pm UTC](https://discourse.itk.org/t/issue-with-the-rtk-output-generated-using-a-head-phantom/6520 "2024-03-19T12:15:36Z")

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Hi, I am trying to reconstruct a CBCT raw data using RTK. I was able to execute the code and generate output, but unfortunately I am facing issues with the output generated. I don’t know if the issue is due to the geome…

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## [ITK Pixel Depth Range Values](https://discourse.itk.org/t/itk-pixel-depth-range-values/6524)

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**Author:** [@kdavet\_sas](https://discourse.itk.org/u/kdavet_sas)\
**Replies:** 1\
**Last updated:** [March 18, 2024, 3:54pm UTC](https://discourse.itk.org/t/itk-pixel-depth-range-values/6524 "2024-03-18T15:54:10Z")

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Hello, I am curious what the pixel depth range values are for ITK images. I found this page that outlines the different file formats and pixel values, but it does not supply the corresponding ranges. For example, these a…

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## [Description: ITK ERROR: Object factory failed to instantiate class itk::RealToHalfHermitianForwardFFTImageFilter\<class itk::Image\<double,3\>,class itk::Image\<class std::complex\<double\>,3\> \>](https://discourse.itk.org/t/description-itk-error-object-factory-failed-to-instantiate-class-itk-realtohalfhermitianforwardfftimagefilter-class-itk-image-double-3-class-itk-image-class-std-complex-double-3/5865)

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**Author:** [@ma1282029525](https://discourse.itk.org/u/ma1282029525)\
**Replies:** 3\
**Last updated:** [March 18, 2024, 6:06am UTC](https://discourse.itk.org/t/description-itk-error-object-factory-failed-to-instantiate-class-itk-realtohalfhermitianforwardfftimagefilter-class-itk-image-double-3-class-itk-image-class-std-complex-double-3/5865 "2024-03-18T06:06:57Z")

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The version attempted to use the RTK library, and there was no problem running the test program. I copied the example in the example and encountered this error.

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## [CUDA version Problem](https://discourse.itk.org/t/cuda-version-problem/6498)

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**Author:** [@skb](https://discourse.itk.org/u/skb)\
**Replies:** 28\
**Last updated:** [March 18, 2024, 12:37am UTC](https://discourse.itk.org/t/cuda-version-problem/6498 "2024-03-18T00:37:38Z")

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i wonder if there are any relationship between the ＣＵＤＡ version of compiling RTK linkｅｄ and the CUDA version of RTK applying environment，because i met a strange problem that a same procedure runs faster on m…

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## [MultiScaleHessianBasedMeasureImageFilter GetScalesOutput() member function doesn't work in python?](https://discourse.itk.org/t/multiscalehessianbasedmeasureimagefilter-getscalesoutput-member-function-doesnt-work-in-python/6518)

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**Author:** [@Chuck\_Hatt](https://discourse.itk.org/u/Chuck_Hatt)\
**Replies:** 2\
**Last updated:** [March 15, 2024, 3:17pm UTC](https://discourse.itk.org/t/multiscalehessianbasedmeasureimagefilter-getscalesoutput-member-function-doesnt-work-in-python/6518 "2024-03-15T15:17:32Z")

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Getting an error when I try write to file or get the numpy array associated with the GetScalesOutput() function for MultiScaleHessianBasedMeasureImageFilter in python. # Load itk\_image from file ImageTyp…

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## [Computing Hessian Eigenvalues in Python: How to interpret output of SymmetricEigenAnalysisImageFilter](https://discourse.itk.org/t/computing-hessian-eigenvalues-in-python-how-to-interpret-output-of-symmetriceigenanalysisimagefilter/6517)

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**Author:** [@Chuck\_Hatt](https://discourse.itk.org/u/Chuck_Hatt)\
**Replies:** 6\
**Last updated:** [March 15, 2024, 2:06pm UTC](https://discourse.itk.org/t/computing-hessian-eigenvalues-in-python-how-to-interpret-output-of-symmetriceigenanalysisimagefilter/6517 "2024-03-15T14:06:28Z")

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Why would the output of SymmetricEigenAnalysisImageFilter have 6 channels, and at each pixel there are more than 3 non-zero values (there should only be three eigenvalues)? This is my code for computing the hessian eige…

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## [Plot TRE per iteration for 2D registration](https://discourse.itk.org/t/plot-tre-per-iteration-for-2d-registration/6505)

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**Author:** [@Vojtech\_Benda](https://discourse.itk.org/u/Vojtech_Benda)\
**Replies:** 4\
**Last updated:** [March 15, 2024, 12:14pm UTC](https://discourse.itk.org/t/plot-tre-per-iteration-for-2d-registration/6505 "2024-03-15T12:14:35Z")

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Hello, I’m trying to plot target registration error (TRE) values at each iteration as shown in this notebook in the Registration cell. The input images are 3D and 2D, where the 3D image is sliced into 2D. They are transf…

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## [How to register a pair of images and their corresponding masks?](https://discourse.itk.org/t/how-to-register-a-pair-of-images-and-their-corresponding-masks/6511)

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**Author:** [@vectorzwt](https://discourse.itk.org/u/vectorzwt)\
**Replies:** 6\
**Last updated:** [March 14, 2024, 7:15am UTC](https://discourse.itk.org/t/how-to-register-a-pair-of-images-and-their-corresponding-masks/6511 "2024-03-14T07:15:08Z")

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Hello everyone.I’m new to simpleitk, and I want to register two images (pre and post surgery) and their corresponding masks. And my code is shown: def rigid\_pre\_post(fixed\_image\_path, moving\_image\_path, fixed\_mask\_path,…

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## [How is origin calculated during resampling?](https://discourse.itk.org/t/how-is-origin-calculated-during-resampling/6515)

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**Author:** [@Xiang\_Zhenyu](https://discourse.itk.org/u/Xiang_Zhenyu)\
**Replies:** 0\
**Last updated:** [March 14, 2024, 6:45am UTC](https://discourse.itk.org/t/how-is-origin-calculated-during-resampling/6515 "2024-03-14T06:45:23Z")

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I want to resample the image to the specified data, but how to calculate the origin so that the image can be displayed normally. Example： origin:(-90.36074829101562, -172.32485961914062, 121.83561706542969) Spacing:(1…

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## [Which image is resampled during registration?](https://discourse.itk.org/t/which-image-is-resampled-during-registration/6512)

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**Author:** [@dstansby](https://discourse.itk.org/u/dstansby)\
**Replies:** 1\
**Last updated:** [March 13, 2024, 6:20pm UTC](https://discourse.itk.org/t/which-image-is-resampled-during-registration/6512 "2024-03-13T18:20:03Z")

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I’m trying to understand how image registration works in SimpleITK, and am unsure which image (fixed or moving) gets interpolated on to the other image during the registration process. As an example, if I’m trying to reg…

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## [Direction loosing negative sign](https://discourse.itk.org/t/direction-loosing-negative-sign/6371)

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**Author:** [@Franciska](https://discourse.itk.org/u/Franciska)\
**Replies:** 5\
**Last updated:** [March 13, 2024, 11:53am UTC](https://discourse.itk.org/t/direction-loosing-negative-sign/6371 "2024-03-13T11:53:45Z")

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I have a nifti file, which if I read with nibabel, and print the affine matrix it looks like this: \[\[-0.28 0. 0. 0. \] \[ 0. -0.28 0. 0. \] \[ 0. 0. 0.28 0. …

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## [Multi-threads registration reproducibility](https://discourse.itk.org/t/multi-threads-registration-reproducibility/4030)

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**Author:** [@Nil](https://discourse.itk.org/u/Nil)\
**Replies:** 17\
**Last updated:** [March 11, 2024, 3:08pm UTC](https://discourse.itk.org/t/multi-threads-registration-reproducibility/4030 "2024-03-11T15:08:15Z")

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I already asked this question on the ANTs project and they told me to ask here. Yes, I have found the ANTs wiki page that explains why the registration is not reproducible. I’m already using a seed. The results are nea…

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## [Can we run itk in wasm without runPipeline?](https://discourse.itk.org/t/can-we-run-itk-in-wasm-without-runpipeline/6437)

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**Author:** [@sedghi](https://discourse.itk.org/u/sedghi)\
**Replies:** 3\
**Last updated:** [March 11, 2024, 12:01pm UTC](https://discourse.itk.org/t/can-we-run-itk-in-wasm-without-runpipeline/6437 "2024-03-11T12:01:42Z")

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My goal is to bring the MorphologicalContourInterpolator to wasm/web Is there a docker image available for itk that we can use to bring itk filters as WASM to the web? The kitware/vtk-wasm docker appears to be quite s…

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## [Why does itk:: CheckerBoardImageFilter flip left and right in the middle position when saving a 3D image](https://discourse.itk.org/t/why-does-itk-checkerboardimagefilter-flip-left-and-right-in-the-middle-position-when-saving-a-3d-image/6506)

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**Author:** [@ma1282029525](https://discourse.itk.org/u/ma1282029525)\
**Replies:** 1\
**Last updated:** [March 11, 2024, 5:51am UTC](https://discourse.itk.org/t/why-does-itk-checkerboardimagefilter-flip-left-and-right-in-the-middle-position-when-saving-a-3d-image/6506 "2024-03-11T05:51:19Z")

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like this

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## [ADMM Reconstruction](https://discourse.itk.org/t/admm-reconstruction/6490)

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**Author:** [@zhangm](https://discourse.itk.org/u/zhangm)\
**Replies:** 13\
**Last updated:** [March 8, 2024, 12:46am UTC](https://discourse.itk.org/t/admm-reconstruction/6490 "2024-03-08T00:46:01Z")

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I successfully ran the FirstCudaReconstruction.py file on my project. But sometimes the scanning angle may only be 90 °, and the reconstruction effect using FDK is not good. I checked the rtk and found that ADMM reconstr…

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## [Transfer from CPUImage to GPUImage](https://discourse.itk.org/t/transfer-from-cpuimage-to-gpuimage/6492)

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**Author:** [@zhangm](https://discourse.itk.org/u/zhangm)\
**Replies:** 3\
**Last updated:** [March 5, 2024, 2:12pm UTC](https://discourse.itk.org/t/transfer-from-cpuimage-to-gpuimage/6492 "2024-03-05T14:12:54Z")

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I need transfer from CPUImage to GPUImage in python. And I find this discourse by use itk.cuda\_image\_to\_image\_filter() to complete the conversion. But the error prompt seems that the fuction only support input type as G…

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## [Tip of the day: How to sync your pull request branch with the master branch](https://discourse.itk.org/t/tip-of-the-day-how-to-sync-your-pull-request-branch-with-the-master-branch/6491)

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**Author:** [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)\
**Replies:** 3\
**Last updated:** [March 5, 2024, 2:09pm UTC](https://discourse.itk.org/t/tip-of-the-day-how-to-sync-your-pull-request-branch-with-the-master-branch/6491 "2024-03-05T14:09:05Z")

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Before pushing a local branch, it’s usually recommended to synchronize the branch with the latest revision of the main branch (the master branch, in the ITK git). While working on my local feature-branch, I often found m…

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## [Error loading DICOM file](https://discourse.itk.org/t/error-loading-dicom-file/6489)

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**Author:** [@Kewil\_Bhima](https://discourse.itk.org/u/Kewil_Bhima)\
**Replies:** 3\
**Last updated:** [March 4, 2024, 8:15pm UTC](https://discourse.itk.org/t/error-loading-dicom-file/6489 "2024-03-04T20:15:38Z")

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I have recently downloaded ITK-Snap and I am having issues loading an image. I get an error saying “vector too long” when trying to load a DICOM file from a MRI scan. I have no issue opening this same image in other soft…

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## [How to generate a .seg.nrrd file out of multiple STL files using Python?](https://discourse.itk.org/t/how-to-generate-a-seg-nrrd-file-out-of-multiple-stl-files-using-python/6484)

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**Author:** [@Dzemal](https://discourse.itk.org/u/Dzemal)\
**Replies:** 2\
**Last updated:** [March 2, 2024, 7:18am UTC](https://discourse.itk.org/t/how-to-generate-a-seg-nrrd-file-out-of-multiple-stl-files-using-python/6484 "2024-03-02T07:18:45Z")

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Hi together, I’ve asked this question also in the Slicer forum and got some help but nevertheless I also want to ask here, maybe there is a another way to implement this issue. I’m trying to write a code snippet in Pyt…

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## [Slow itkContourExtractor2DImageFilter](https://discourse.itk.org/t/slow-itkcontourextractor2dimagefilter/6486)

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**Author:** [@finetjul](https://discourse.itk.org/u/finetjul)\
**Replies:** 0\
**Last updated:** [March 1, 2024, 3:58pm UTC](https://discourse.itk.org/t/slow-itkcontourextractor2dimagefilter/6486 "2024-03-01T15:58:57Z")

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Hi, itkContourExtractor2DImageFilter is slow for our need. Is there a way to configure it to speed it up (e.g. we could provide a seed to the algorithm for what contour to extract) ? Is there an alternative algorithm th…

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## [How to get image mask in simpleitk?](https://discourse.itk.org/t/how-to-get-image-mask-in-simpleitk/6470)

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**Author:** [@dstansby](https://discourse.itk.org/u/dstansby)\
**Replies:** 4\
**Last updated:** [February 29, 2024, 9:29pm UTC](https://discourse.itk.org/t/how-to-get-image-mask-in-simpleitk/6470 "2024-02-29T21:29:59Z")

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I’m trying to set and get a mask on an image using simpleitk in Python. I’m setting the mask like this: image: sitk.Image mask: npt.NDArray masked\_image = sitk.Mask(image, sitk.GetImageFromArray(mask)) I can’t work out…

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## [MHA File Format Question about Transform Matrix](https://discourse.itk.org/t/mha-file-format-question-about-transform-matrix/6481)

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**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 1\
**Last updated:** [February 29, 2024, 4:59pm UTC](https://discourse.itk.org/t/mha-file-format-question-about-transform-matrix/6481 "2024-02-29T16:59:36Z")

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Looking at the header for the .MHA file format there is a Transform Matrix encoded in there. We use the ITK Image reader classes to get at this information. metaImageIO-\>SetFileName(filePath); metaImageIO-\>ReadI…

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## [ITK Training Course in March](https://discourse.itk.org/t/itk-training-course-in-march/6474)

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**Author:** [@finetjul](https://discourse.itk.org/u/finetjul)\
**Replies:** 2\
**Last updated:** [February 28, 2024, 7:05am UTC](https://discourse.itk.org/t/itk-training-course-in-march/6474 "2024-02-28T07:05:24Z")

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Kitware Europe will be holding an online/onsite developer’s training course on March 11th 2024 in Lyon, France. This course will cover features of ITK : Overview/Architecture Segmentation Registration Using ITK in you…

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## [Where can I find the compiled C++ dynamic library?](https://discourse.itk.org/t/where-can-i-find-the-compiled-c-dynamic-library/6475)

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**Author:** [@didididi2001](https://discourse.itk.org/u/didididi2001)\
**Replies:** 0\
**Last updated:** [February 27, 2024, 6:17pm UTC](https://discourse.itk.org/t/where-can-i-find-the-compiled-c-dynamic-library/6475 "2024-02-27T18:17:19Z")

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My own device compiles very slowly. I want to know where I can find dynamic library files compiled by various platforms. I see that there are scripts to compile in this project, and someone has compiled it. Where can I f…

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## [Fusion between segmentation and reference image](https://discourse.itk.org/t/fusion-between-segmentation-and-reference-image/6469)

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**Author:** [@Nuno\_Loucao1](https://discourse.itk.org/u/Nuno_Loucao1)\
**Replies:** 1\
**Last updated:** [February 26, 2024, 4:09pm UTC](https://discourse.itk.org/t/fusion-between-segmentation-and-reference-image/6469 "2024-02-26T16:09:19Z")

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Hi! I’m performing an analysis on a 4D breast MRI scan. I’m trying to fuse the segmentation results on a reference image dataset (3D), but without results. So i have the lesion segmented, then i multiply it by, p.ex.,…

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## [Metal Artifacts detection](https://discourse.itk.org/t/metal-artifacts-detection/6467)

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**Author:** [@pratibha](https://discourse.itk.org/u/pratibha)\
**Replies:** 2\
**Last updated:** [February 26, 2024, 3:45pm UTC](https://discourse.itk.org/t/metal-artifacts-detection/6467 "2024-02-26T15:45:05Z")

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Hello, I just need to detect metal artifacts not reconstruct. Could you recommend any papers or resources where I could get an idea of this? In addition to metal artifacts, I have other artifacts on my data, such as ali…

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