# Beginner Questions **URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=13 [Latest](https://discourse.itk.org/latest.md) · [Categories](https://discourse.itk.org/categories.md) · [Tags](https://discourse.itk.org/tags.md) **Page:** 14 --- ## [Apply deformation to the 3D-CT image volume from mesh displacement](https://discourse.itk.org/t/apply-deformation-to-the-3d-ct-image-volume-from-mesh-displacement/5338)
**Author:** [@lakmy](https://discourse.itk.org/u/lakmy)\ **Replies:** 1\ **Last updated:** [September 16, 2022, 3:30pm UTC](https://discourse.itk.org/t/apply-deformation-to-the-3d-ct-image-volume-from-mesh-displacement/5338 "2022-09-16T15:30:23Z")
I have a reference mesh and a deformed version of it (they are unstrcuted grid saved in vtk file format). The reference mesh was acquired from a 3D-CT volume. I would want to apply the same deformation to the reference … --- ## [Which of path should set to ITK\_DIR](https://discourse.itk.org/t/which-of-path-should-set-to-itk-dir/4675)
**Author:** [@xh\_c](https://discourse.itk.org/u/xh_c)\ **Replies:** 8\ **Last updated:** [September 14, 2022, 8:22pm UTC](https://discourse.itk.org/t/which-of-path-should-set-to-itk-dir/4675 "2022-09-14T20:22:25Z")
Hello, I just build ITK with cmake. Now I have two folder, ITK\_source and ITK\_build. I set my ITK\_DIR to ITK\_build but get no head file error. And I found that some ITK module just have .obj file and no .cxx or .h. In IT… --- ## [3D multi-modal medical image registration using user defined function for similarity metric computation](https://discourse.itk.org/t/3d-multi-modal-medical-image-registration-using-user-defined-function-for-similarity-metric-computation/5064)
**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\ **Replies:** 41\ **Last updated:** [September 10, 2022, 3:41pm UTC](https://discourse.itk.org/t/3d-multi-modal-medical-image-registration-using-user-defined-function-for-similarity-metric-computation/5064 "2022-09-10T15:41:02Z")
Hello, I want to register two 3D multi-modal medical images using mutual information. However instead of using the inbuilt MattesMutualInformation or JointHistogramMutualInformation, I want to use my own mutual informat… --- ## [Getting 3D images from stacking 2D axial slices with all important coordinate information](https://discourse.itk.org/t/getting-3d-images-from-stacking-2d-axial-slices-with-all-important-coordinate-information/5313)
**Author:** [@shadab](https://discourse.itk.org/u/shadab)\ **Replies:** 0\ **Last updated:** [September 2, 2022, 6:27pm UTC](https://discourse.itk.org/t/getting-3d-images-from-stacking-2d-axial-slices-with-all-important-coordinate-information/5313 "2022-09-02T18:27:36Z")
Hi ITK community, I have a 3D PET/CT dataset with 3D segmentations (GT) (with labels 0, 1, and 2). The CT images are typically 512x512xSizeZ, while the PET images are of various shapes like 128x128xSizeZ' or \`256x256xSi… --- ## [Installation problem (ITK3.2.0 in Linux)](https://discourse.itk.org/t/installation-problem-itk3-2-0-in-linux/724)
**Author:** [@LiuHao-THU](https://discourse.itk.org/u/LiuHao-THU)\ **Replies:** 4\ **Last updated:** [August 30, 2022, 7:51pm UTC](https://discourse.itk.org/t/installation-problem-itk3-2-0-in-linux/724 "2022-08-30T19:51:18Z")
hi, i am a beginner to ITK, now I am installing itk(3.2) vtk(5.8) in my Linux. and I meet some problem. I even do not know how to solve it. I have successfully installed the latest version ITK and vtk, however the lates… --- ## [How to apply mask when using rescale filter](https://discourse.itk.org/t/how-to-apply-mask-when-using-rescale-filter/5295)
**Author:** [@willi3by](https://discourse.itk.org/u/willi3by)\ **Replies:** 5\ **Last updated:** [August 29, 2022, 1:58pm UTC](https://discourse.itk.org/t/how-to-apply-mask-when-using-rescale-filter/5295 "2022-08-29T13:58:15Z")
Hi, I am implementing a modified version of the filtering approach in this tutorial: Segment Blood Vessels With Multi-Scale Hessian-Based Measure — v5.3.0 However, my images contain tissue for which I do not want to app… --- ## [Is it possible to apply transformation to other images?](https://discourse.itk.org/t/is-it-possible-to-apply-transformation-to-other-images/5302)
**Author:** [@GrowlingM1ke](https://discourse.itk.org/u/GrowlingM1ke)\ **Replies:** 1\ **Last updated:** [August 29, 2022, 1:07pm UTC](https://discourse.itk.org/t/is-it-possible-to-apply-transformation-to-other-images/5302 "2022-08-29T13:07:43Z")
Hello, I’ve been using pyelastix toolkit in order to perform non-rigid image registration. I needed to boost the contrast within the images I was using in order to improve registration, however the pyelastix wrapper doe… --- ## [itk-wasm wasi build for c++ program](https://discourse.itk.org/t/itk-wasm-wasi-build-for-c-program/5153)
**Author:** [@sag](https://discourse.itk.org/u/sag)\ **Replies:** 3\ **Last updated:** [August 26, 2022, 5:44pm UTC](https://discourse.itk.org/t/itk-wasm-wasi-build-for-c-program/5153 "2022-08-26T17:44:10Z")
@matt.mccormick , @dzenanz , Hi, I need help to link hdf5 libraries of ITK-5.2.1/ITK-5.3 to a itk-wasm/wasi build. It seems to complain about hdf5 libraries. the c++ code: include \ causes the fd… --- ## [ITK-JS && ITK-WASM](https://discourse.itk.org/t/itk-js-itk-wasm/5021)
**Author:** [@sag](https://discourse.itk.org/u/sag)\ **Replies:** 14\ **Last updated:** [August 26, 2022, 2:01pm UTC](https://discourse.itk.org/t/itk-js-itk-wasm/5021 "2022-08-26T14:01:54Z")
@matt.mccormick Hi Mat, I am trying to use both ITK-JS and ITK-WASM. I have failed in both. please help me with following questions: +I have followed this Node.js HelloWorld, and i failed with the error cannot find mo… --- ## [C order or F order？](https://discourse.itk.org/t/c-order-or-f-order/5287)
**Author:** [@liguangops](https://discourse.itk.org/u/liguangops)\ **Replies:** 7\ **Last updated:** [August 26, 2022, 1:09pm UTC](https://discourse.itk.org/t/c-order-or-f-order/5287 "2022-08-26T13:09:21Z")
I have a 3d dicom nii.gz file with shape \[900,900,500\]. And I read it by using itk::ImageReader. Then I want to split it into 6480 with shapes \[50,50,25\] by moving ImageBufferPointer. But I don’t know if the order in me… --- ## [Is instance number used to collect dicom series?](https://discourse.itk.org/t/is-instance-number-used-to-collect-dicom-series/5283)
**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\ **Replies:** 5\ **Last updated:** [August 24, 2022, 1:54am UTC](https://discourse.itk.org/t/is-instance-number-used-to-collect-dicom-series/5283 "2022-08-24T01:54:52Z")
Usually, I use Instance Number to collect dicom series, just like: imgs\[ key \] = dicomImg where key is the Instance Number, and dicomImg is the dicom information (header/pixel array). However, sometimes, I find that t… --- ## [4D and 3D + t images](https://discourse.itk.org/t/4d-and-3d-t-images/5288)
**Author:** [@Farah](https://discourse.itk.org/u/Farah)\ **Replies:** 1\ **Last updated:** [August 23, 2022, 12:47pm UTC](https://discourse.itk.org/t/4d-and-3d-t-images/5288 "2022-08-23T12:47:13Z")
Hi, I have 4D CT dataset that is basically lots of DCM files (DICOM), each group of DCMs present a 3D volume phase in the cardiac cycle, so I ended up with 10 3D volumes, I don’t know if this is assumed as 3D + t or 4D … --- ## [Problem realated to ITK.JS WebWorkers/ImageIO.worker.js](https://discourse.itk.org/t/problem-realated-to-itk-js-webworkers-imageio-worker-js/5216)
**Author:** [@Yuvi-416](https://discourse.itk.org/u/Yuvi-416)\ **Replies:** 2\ **Last updated:** [August 23, 2022, 12:15am UTC](https://discourse.itk.org/t/problem-realated-to-itk-js-webworkers-imageio-worker-js/5216 "2022-08-23T00:15:11Z")
Hello everyone, I am trying to run the below code to read a series of DICOM images and convert them into VTK objects before I send them for visualization. Problem is that, sometimes, itk.js read the image but most of t… --- ## [How to \`itk.resample\_image\_filter\` with a \`BSplineTransform\` with 3D images?](https://discourse.itk.org/t/how-to-itk-resample-image-filter-with-a-bsplinetransform-with-3d-images/4987)
**Author:** [@edgar](https://discourse.itk.org/u/edgar)\ **Replies:** 11\ **Last updated:** [August 16, 2022, 9:06am UTC](https://discourse.itk.org/t/how-to-itk-resample-image-filter-with-a-bsplinetransform-with-3d-images/4987 "2022-08-16T09:06:57Z")
Table of Contents 1. How to itk.resample\_image\_filter with a BSplineTransform with 3D images? 1.1. What I have tried 1.1.1. Inputs (data) 1.1.2. Failed attempt with resample\_image\_filter 1.1.3. Useless result wit… --- ## [how to read a multi-frame DICOM with itk-wasm](https://discourse.itk.org/t/how-to-read-a-multi-frame-dicom-with-itk-wasm/5029)
**Author:** [@maoweihang1995](https://discourse.itk.org/u/maoweihang1995)\ **Replies:** 6\ **Last updated:** [August 15, 2022, 9:06pm UTC](https://discourse.itk.org/t/how-to-read-a-multi-frame-dicom-with-itk-wasm/5029 "2022-08-15T21:06:42Z")
I want to read a multi frame DICOM file with the API of readImageFile，but it doesn’t work。And it is normal to read a single frame file. And using the demo also doesn’t work.I wonder if itk-wasm does not support multi f… --- ## [GetMatrix from SimpleITK ImageRegistrationMethod.Execute transform result](https://discourse.itk.org/t/getmatrix-from-simpleitk-imageregistrationmethod-execute-transform-result/5256)
**Author:** [@ktdiedrich](https://discourse.itk.org/u/ktdiedrich)\ **Replies:** 2\ **Last updated:** [August 15, 2022, 2:51pm UTC](https://discourse.itk.org/t/getmatrix-from-simpleitk-imageregistrationmethod-execute-transform-result/5256 "2022-08-15T14:51:32Z")
Is there a way to GetMatrix from the base transform returned from ImageRegistrationMethod.Execute(…)? final\_transform = registration\_method.Execute(fixed\_image, moving\_image) Final\_transform doesn’t have access to GetM… --- ## [Exception occured during image io error](https://discourse.itk.org/t/exception-occured-during-image-io-error/5259)
**Author:** [@mahesh\_bhosale](https://discourse.itk.org/u/mahesh_bhosale)\ **Replies:** 1\ **Last updated:** [August 15, 2022, 12:50pm UTC](https://discourse.itk.org/t/exception-occured-during-image-io-error/5259 "2022-08-15T12:50:25Z")
Hi, I have been trying to load the predicted segmentation mask, which is a 3d PyTorch tensor saved as a nifty file, but I am getting below error. I am actually able to load the image volumes stored in a similar manner b… --- ## [Confocal imaging alignment](https://discourse.itk.org/t/confocal-imaging-alignment/5252)
**Author:** [@mixail\_orfanakis](https://discourse.itk.org/u/mixail_orfanakis)\ **Replies:** 1\ **Last updated:** [August 10, 2022, 2:10am UTC](https://discourse.itk.org/t/confocal-imaging-alignment/5252 "2022-08-10T02:10:36Z")
Hallo everyone, I am trying to align different images obtained either from confocal microscopy or from vectra polaris. I am using the Simple ITK imaris python extension, but since I do not have any idea of how the algor… --- ## [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… --- ## [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 … --- ## [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. --- ## [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… --- ## [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… --- ## [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,… --- ## [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… [Previous page](https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=12) [Next page](https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=14)