# Latest **URL:** https://discourse.itk.org/latest.md?page=35 [Latest](https://discourse.itk.org/latest.md) · [Categories](https://discourse.itk.org/categories.md) · [Tags](https://discourse.itk.org/tags.md) **Page:** 36 --- ## [Proper way to resample a 3D image](https://discourse.itk.org/t/proper-way-to-resample-a-3d-image/5227)
**Author:** [@chlee](https://discourse.itk.org/u/chlee)\ **Replies:** 2\ **Last updated:** [August 3, 2022, 11:15pm UTC](https://discourse.itk.org/t/proper-way-to-resample-a-3d-image/5227 "2022-08-03T23:15:32Z")
Hi, I have acquired my 3D image z-stack, from z=0 to z=70, total of 71 slices on the z-axis. I have another image that I had a spacing of 2, and acquired from z=0 to z=70, so 36 slices on the z-axis. I am following the… --- ## [bspline registration from numpy array doesn't transform point](https://discourse.itk.org/t/bspline-registration-from-numpy-array-doesnt-transform-point/5238)
**Author:** [@Ilay\_Kamai](https://discourse.itk.org/u/Ilay_Kamai)\ **Replies:** 0\ **Last updated:** [August 3, 2022, 7:27pm UTC](https://discourse.itk.org/t/bspline-registration-from-numpy-array-doesnt-transform-point/5238 "2022-08-03T19:27:41Z")
Hi, i’m registering two DICOM images using affine and Bspline registrations. after registration, I’m using the transformation to transform points (in physical space). I’m creating an interactive interface that enable t… --- ## [Finding the largest physical region (bounding box) across an arbitrary number of input files (SimpleITK)](https://discourse.itk.org/t/finding-the-largest-physical-region-bounding-box-across-an-arbitrary-number-of-input-files-simpleitk/5234)
**Author:** [@gdevenyi](https://discourse.itk.org/u/gdevenyi)\ **Replies:** 5\ **Last updated:** [August 2, 2022, 10:52pm UTC](https://discourse.itk.org/t/finding-the-largest-physical-region-bounding-box-across-an-arbitrary-number-of-input-files-simpleitk/5234 "2022-08-02T22:52:16Z")
I’m working on an arbitrary image averaging script, where I’d like to assume input images are not guaranteed to overlap (completely, or even partially). As such, I need to construct a “common” space which contains all th… --- ## [SimpleITK 2.2 Release Candidate 4](https://discourse.itk.org/t/simpleitk-2-2-release-candidate-4/5226)
**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\ **Replies:** 6\ **Last updated:** [August 1, 2022, 5:19pm UTC](https://discourse.itk.org/t/simpleitk-2-2-release-candidate-4/5226 "2022-08-01T17:19:50Z")
Announcing the SimpleITK 2.2 Release Candidate 4! Users and developers are encouraged to test the RC before the final release and report issues, bugs, and any compatibility problems. This is the final RC before the 2.2 … --- ## [Watershed segmentation algorithms](https://discourse.itk.org/t/watershed-segmentation-algorithms/5235)
**Author:** [@chlee](https://discourse.itk.org/u/chlee)\ **Replies:** 0\ **Last updated:** [August 2, 2022, 8:04am UTC](https://discourse.itk.org/t/watershed-segmentation-algorithms/5235 "2022-08-02T08:04:45Z")
Thank you so much for all the input, I am learning so much from this site. I see that there are several watershed segmentation filter examples out there: Watershed Image Filter Morphological Watershed segmentation Mo… --- ## [Ball Binary Morphological filter with different spacing?](https://discourse.itk.org/t/ball-binary-morphological-filter-with-different-spacing/5228)
**Author:** [@chlee](https://discourse.itk.org/u/chlee)\ **Replies:** 2\ **Last updated:** [August 2, 2022, 7:55am UTC](https://discourse.itk.org/t/ball-binary-morphological-filter-with-different-spacing/5228 "2022-08-02T07:55:37Z")
Hi, I want to generate a segmented image and want to do a 3D morphological closing operation just before the thresholding event. I already have a binary 3D image. The issue is that my 3D image x,y,z spacing is not same … --- ## [DiscreteGaussianImageFilter with RGBPixel](https://discourse.itk.org/t/discretegaussianimagefilter-with-rgbpixel/5231)
**Author:** [@Matthieu\_Brucher](https://discourse.itk.org/u/Matthieu_Brucher)\ **Replies:** 4\ **Last updated:** [August 1, 2022, 6:35pm UTC](https://discourse.itk.org/t/discretegaussianimagefilter-with-rgbpixel/5231 "2022-08-01T18:35:46Z")
Is it possible to natively get an image with RGBPixel\<\> as the internal type filtered with this filter? Looks like there are some issues with ITK 5.2.0, as the intermediate type messes up the setup and stops with: /opt… --- ## [how to convert a tensor with libtorch into a ITK image?](https://discourse.itk.org/t/how-to-convert-a-tensor-with-libtorch-into-a-itk-image/5176)
**Author:** [@Bugmaker](https://discourse.itk.org/u/Bugmaker)\ **Replies:** 10\ **Last updated:** [August 1, 2022, 8:34am UTC](https://discourse.itk.org/t/how-to-convert-a-tensor-with-libtorch-into-a-itk-image/5176 "2022-08-01T08:34:29Z")
I have created a tensor by libtorch , which it’s shape is 688,688,450, and I want to transfer this tensor into image. --- ## [Did ITK can read a directory of one serial that of many files, and write into one dcm file of multi frames.](https://discourse.itk.org/t/did-itk-can-read-a-directory-of-one-serial-that-of-many-files-and-write-into-one-dcm-file-of-multi-frames/5213)
**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\ **Replies:** 2\ **Last updated:** [July 29, 2022, 11:16pm UTC](https://discourse.itk.org/t/did-itk-can-read-a-directory-of-one-serial-that-of-many-files-and-write-into-one-dcm-file-of-multi-frames/5213 "2022-07-29T23:16:48Z")
Now I have a CT serial in a directory, now I want to read all the serial files and write it into one single dcm file. --- ## [Brainstorming ideas: Better Overlay Experience in Jupyter Notebooks](https://discourse.itk.org/t/brainstorming-ideas-better-overlay-experience-in-jupyter-notebooks/4514)
**Author:** [@kolibril13](https://discourse.itk.org/u/kolibril13)\ **Replies:** 1\ **Last updated:** [July 29, 2022, 8:28pm UTC](https://discourse.itk.org/t/brainstorming-ideas-better-overlay-experience-in-jupyter-notebooks/4514 "2022-07-29T20:28:54Z")
While iterating on a segmentation workflow, it is good to have a previous/after view. Currently, that can be done with an overlay or displaying the pictures left and right. I just want to propose some ideas that would … --- ## [itk-wasm, wasi build, how to run the .wasm.wasi passing \ \ \](https://discourse.itk.org/t/itk-wasm-wasi-build-how-to-run-the-wasm-wasi-passing-inputimage-outputimage-radius/5225)
**Author:** [@sag](https://discourse.itk.org/u/sag)\ **Replies:** 0\ **Last updated:** [July 29, 2022, 1:55pm UTC](https://discourse.itk.org/t/itk-wasm-wasi-build-how-to-run-the-wasm-wasi-passing-inputimage-outputimage-radius/5225 "2022-07-29T13:55:26Z")
Hi @dzenanz, I have failed to build wasi using itk-wasm for a ITK Median Filter. here is the screen shot of the wasi build for MedianFilterTest pipeline, CMakeLists seems to have problem for wasi-build because as you se… --- ## [largestpossibile region is bigger than request region and m\_buffered region](https://discourse.itk.org/t/largestpossibile-region-is-bigger-than-request-region-and-m-buffered-region/5222)
**Author:** [@Bugmaker](https://discourse.itk.org/u/Bugmaker)\ **Replies:** 3\ **Last updated:** [July 29, 2022, 1:23am UTC](https://discourse.itk.org/t/largestpossibile-region-is-bigger-than-request-region-and-m-buffered-region/5222 "2022-07-29T01:23:23Z")
hi I load a nii.gz file using ITK, and I find this file\`s largest possible region(531,531,604) is bigger than request and m\_buffer region (both of them are 512,512,604). I know this can be fixed by setrequest() or setmy… --- ## [How to add Patient Position tag (Origin) to each slice in a SimpleITK image?](https://discourse.itk.org/t/how-to-add-patient-position-tag-origin-to-each-slice-in-a-simpleitk-image/5218)
**Author:** [@lbrandao](https://discourse.itk.org/u/lbrandao)\ **Replies:** 2\ **Last updated:** [July 28, 2022, 3:26pm UTC](https://discourse.itk.org/t/how-to-add-patient-position-tag-origin-to-each-slice-in-a-simpleitk-image/5218 "2022-07-28T15:26:02Z")
I have a multi-slice volume \[shape (256,256,14)\] stored in a .vtk file. The header of the file, contains the following information: # vtk DataFile Version 3.0 vtk output BINARY DATASET STRUCTURED\_POINTS DIMENSIONS 2… --- ## [MedianFilterTest, ITK-WASM, ITK-JS, ITK-JS-VTK, crashed when running npx node index.mjs ./cthead.png ./cthead1.out.png 4](https://discourse.itk.org/t/medianfiltertest-itk-wasm-itk-js-itk-js-vtk-crashed-when-running-npx-node-index-mjs-cthead-png-cthead1-out-png-4/5223)
**Author:** [@sag](https://discourse.itk.org/u/sag)\ **Replies:** 2\ **Last updated:** [July 28, 2022, 12:29pm UTC](https://discourse.itk.org/t/medianfiltertest-itk-wasm-itk-js-itk-js-vtk-crashed-when-running-npx-node-index-mjs-cthead-png-cthead1-out-png-4/5223 "2022-07-28T12:29:30Z")
Hi @dzenanz, I am stuck in ITK-JS, ITK-WASM. Environment: VSCODE: latest version Node version: node.js 16.15.1 npm version: 8.11.0 EDI: Visual studio code/WSL2(widows linux subsystem) works fine. docker desktop: i… --- ## [Running ITK-Snap with image and segmentation by Simple ITK Image Viewer Class](https://discourse.itk.org/t/running-itk-snap-with-image-and-segmentation-by-simple-itk-image-viewer-class/5215)
**Author:** [@Oguzcan13](https://discourse.itk.org/u/Oguzcan13)\ **Replies:** 1\ **Last updated:** [July 27, 2022, 7:16pm UTC](https://discourse.itk.org/t/running-itk-snap-with-image-and-segmentation-by-simple-itk-image-viewer-class/5215 "2022-07-27T19:16:51Z")
Hi there my question is quite basic actually but I couldn’t find the is there any way or not? I have Dicom image series and Prediction of Segmentation with .jpeg files. Basically, I am able to read them by SimpleITK but… --- ## [Are there any image harmonization modules in sitk?](https://discourse.itk.org/t/are-there-any-image-harmonization-modules-in-sitk/5219)
**Author:** [@DushiFdo](https://discourse.itk.org/u/DushiFdo)\ **Replies:** 2\ **Last updated:** [July 26, 2022, 8:14pm UTC](https://discourse.itk.org/t/are-there-any-image-harmonization-modules-in-sitk/5219 "2022-07-26T20:14:42Z")
Hi, I am working on 3D CT images (128x128x128) where the region of interest is liver. I am trying to apply harmonization methods on 3D volumes where my features are voxel intensities. I first tried neurocombat (GitHub … --- ## [Compile time is very long -- how to optimize?](https://discourse.itk.org/t/compile-time-is-very-long-how-to-optimize/5196)
**Author:** [@gmm9uf](https://discourse.itk.org/u/gmm9uf)\ **Replies:** 8\ **Last updated:** [July 26, 2022, 4:03pm UTC](https://discourse.itk.org/t/compile-time-is-very-long-how-to-optimize/5196 "2022-07-26T16:03:43Z")
I am using cmake and make to build and compile C++ code on a linux interface. Each time I want to modify the code and recompile (i.e., make), it takes about 20 minutes to recompile using make. Does anyone know why this w… --- ## [Is there a subset and combine filter?](https://discourse.itk.org/t/is-there-a-subset-and-combine-filter/5212)
**Author:** [@chlee](https://discourse.itk.org/u/chlee)\ **Replies:** 4\ **Last updated:** [July 26, 2022, 2:28pm UTC](https://discourse.itk.org/t/is-there-a-subset-and-combine-filter/5212 "2022-07-26T14:28:10Z")
Hi, I very much appreciate for any tips, just started using the ITK. Not to re-invent the wheel, may I ask whether there are any filters that subset a 3D image along slices (say take z=5-10), process through filters, an… --- ## [set up itk with visual studio and Cmake](https://discourse.itk.org/t/set-up-itk-with-visual-studio-and-cmake/1772)
**Author:** [@abir](https://discourse.itk.org/u/abir)\ **Replies:** 4\ **Last updated:** [July 25, 2022, 1:29pm UTC](https://discourse.itk.org/t/set-up-itk-with-visual-studio-and-cmake/1772 "2022-07-25T13:29:09Z")
I have been trying to set up itk and got a problem while Itried to run Cmake on a HelloWorld project . I can’t figure out what’s the problem exactly !! --- ## [How to derive quantile value of a particular threshold value](https://discourse.itk.org/t/how-to-derive-quantile-value-of-a-particular-threshold-value/5199)
**Author:** [@chlee](https://discourse.itk.org/u/chlee)\ **Replies:** 10\ **Last updated:** [July 23, 2022, 1:51am UTC](https://discourse.itk.org/t/how-to-derive-quantile-value-of-a-particular-threshold-value/5199 "2022-07-23T01:51:00Z")
Hi, I am using ITK C++, and I have applied Otsu thresholding to derive a threshold for a particular image. Now, I want to know the quantile this threshold is set. What would be the best way to do this? Also, ultimately,… --- ## [Extract contours from 3D image](https://discourse.itk.org/t/extract-contours-from-3d-image/5209)
**Author:** [@Kap](https://discourse.itk.org/u/Kap)\ **Replies:** 2\ **Last updated:** [July 22, 2022, 6:39pm UTC](https://discourse.itk.org/t/extract-contours-from-3d-image/5209 "2022-07-22T18:39:10Z")
Dears, I am trying to extract the contour from an object after the procedure of the segmentation. The complie is error free but the output is an empty(black) image. Maybe the output image type is wrong ? Any ideas ? H… --- ## [File written with libminc not readable in ITK?](https://discourse.itk.org/t/file-written-with-libminc-not-readable-in-itk/5192)
**Author:** [@shai-ikko](https://discourse.itk.org/u/shai-ikko)\ **Replies:** 6\ **Last updated:** [July 21, 2022, 2:03pm UTC](https://discourse.itk.org/t/file-written-with-libminc-not-readable-in-itk/5192 "2022-07-21T14:03:27Z")
Hi, this is my first question here. I’m trying to write some MNC2 files for them to be later viewed in Slicer 3D, and I run into a very odd problem: The file I’m writing with code that uses libminc directly, which seems… --- ## [Building vtkITK Lib with Emscripten](https://discourse.itk.org/t/building-vtkitk-lib-with-emscripten/3908)
**Author:** [@Andrzej\_Marciniak](https://discourse.itk.org/u/Andrzej_Marciniak)\ **Replies:** 5\ **Last updated:** [July 21, 2022, 9:55am UTC](https://discourse.itk.org/t/building-vtkitk-lib-with-emscripten/3908 "2022-07-21T09:55:07Z")
I just read @matt.mccormick answer to @prashanth.dumpuri about building with Emscripten for beginners (https://discourse.itk.org/t/building-itk-with-emscripten/2919/5) and it helped me a lot. I am using insighttoolkit… --- ## [Comparing ITK images efficiently.](https://discourse.itk.org/t/comparing-itk-images-efficiently/5203)
**Author:** [@Seun](https://discourse.itk.org/u/Seun)\ **Replies:** 9\ **Last updated:** [July 20, 2022, 8:27pm UTC](https://discourse.itk.org/t/comparing-itk-images-efficiently/5203 "2022-07-20T20:27:50Z")
Hello everyone, I was wondering what would be the fastest way in comparing 2 ITK images irrespective of how large the images are. For instance if I have 2 images both 1000x1000 and I would like to make sure they are exa… --- ## [shapeOpeningLabelMapFilter](https://discourse.itk.org/t/shapeopeninglabelmapfilter/5183)
**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\ **Replies:** 7\ **Last updated:** [July 20, 2022, 12:10pm UTC](https://discourse.itk.org/t/shapeopeninglabelmapfilter/5183 "2022-07-20T12:10:07Z")
I am using shapeOpeningLabelMapFilter and I am getting a strange message saying the attributes are not a member of ShapeOpeningLabelMapFilter. /usr/local/include/ITK-5.2/itkShapeOpeningLabelMapFilter.hxx:44:5: error: ‘… --- ## [Integrate itk-wasm with VTK example](https://discourse.itk.org/t/integrate-itk-wasm-with-vtk-example/5101)
**Author:** [@Albers\_Steven](https://discourse.itk.org/u/Albers_Steven)\ **Replies:** 2\ **Last updated:** [July 19, 2022, 2:11pm UTC](https://discourse.itk.org/t/integrate-itk-wasm-with-vtk-example/5101 "2022-07-19T14:11:43Z")
I want to try VTK C++ ClipUnstructuredGridWithPlane example with itk-wasm just like Hello World hello.cxx. After download ClipUnstructuredGridWithPlane example file and npm install itk-wasm globel. I run itk-wasm build … --- ## [ITK 5.2, WASM, itk-wasm, itk-wasm/emscripten, build example common/add noise to Binary Image, yinyang](https://discourse.itk.org/t/itk-5-2-wasm-itk-wasm-itk-wasm-emscripten-build-example-common-add-noise-to-binary-image-yinyang/5197)
**Author:** [@sag](https://discourse.itk.org/u/sag)\ **Replies:** 0\ **Last updated:** [July 19, 2022, 11:29am UTC](https://discourse.itk.org/t/itk-5-2-wasm-itk-wasm-itk-wasm-emscripten-build-example-common-add-noise-to-binary-image-yinyang/5197 "2022-07-19T11:29:10Z")
@matt.mccormick, Hi everyone, subject: extend HelloWorld web-build example so that i can build itk example common/add noise to Binary Image, yinyang.png using node. couple of questions please bear with me. itk-wasm i… --- ## [Wired ResampleImageFilter results after downsampling a 3D image and then upsampling it to the original size](https://discourse.itk.org/t/wired-resampleimagefilter-results-after-downsampling-a-3d-image-and-then-upsampling-it-to-the-original-size/5193)
**Author:** [@Ruoyan](https://discourse.itk.org/u/Ruoyan)\ **Replies:** 6\ **Last updated:** [July 18, 2022, 9:33pm UTC](https://discourse.itk.org/t/wired-resampleimagefilter-results-after-downsampling-a-3d-image-and-then-upsampling-it-to-the-original-size/5193 "2022-07-18T21:33:47Z")
Hi, I’m trying to downsample an image to 50\*50\*50 and then upsample it back to the original size. After I processed this with two ResampleImageFilter, the new upsampled image has 2\*z\_size\*y\_size black/empty pixels at … --- ## [VersorTransformation does not work correctly with CompositeTransform after version 2.0.0](https://discourse.itk.org/t/versortransformation-does-not-work-correctly-with-compositetransform-after-version-2-0-0/5194)
**Author:** [@rraayyii](https://discourse.itk.org/u/rraayyii)\ **Replies:** 11\ **Last updated:** [July 18, 2022, 7:12pm UTC](https://discourse.itk.org/t/versortransformation-does-not-work-correctly-with-compositetransform-after-version-2-0-0/5194 "2022-07-18T19:12:39Z")
My code with VersorTransform & CompositeTransform doesn’t work anymore after I updated SimpleITK from 1.2.4 to anything above 2.0.0. Diving into the issue, I found that for some reason by adding VersorTransform into a C… --- ## [simple ITK in windows container](https://discourse.itk.org/t/simple-itk-in-windows-container/5169)
**Author:** [@Sowmya\_Rajesh](https://discourse.itk.org/u/Sowmya_Rajesh)\ **Replies:** 5\ **Last updated:** [July 18, 2022, 6:45pm UTC](https://discourse.itk.org/t/simple-itk-in-windows-container/5169 "2022-07-18T18:45:26Z")
I am trying to use simpleITK inside the docker windows container. The container is built without any error. But when I run the container, I am getting the following error. Traceback (most recent call last): File “c:\\h… [Previous page](https://discourse.itk.org/latest.md?page=34) [Next page](https://discourse.itk.org/latest.md?page=36)