# Beginner Questions **URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false [Latest](https://discourse.itk.org/latest.md) · [Categories](https://discourse.itk.org/categories.md) · [Tags](https://discourse.itk.org/tags.md) --- ## [About the Beginner Questions category](https://discourse.itk.org/t/about-the-beginner-questions-category/28)
**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\ **Replies:** 0\ **Last updated:** [September 15, 2017, 6:21pm UTC](https://discourse.itk.org/t/about-the-beginner-questions-category/28 "2017-09-15T18:21:37Z")
Ask your first question! --- ## [Best approach for analyzing microscope images with ITK?](https://discourse.itk.org/t/best-approach-for-analyzing-microscope-images-with-itk/7799)
**Author:** [@Alexia\_Fison](https://discourse.itk.org/u/Alexia_Fison)\ **Replies:** 2\ **Last updated:** [September 9, 2026, 1:03pm UTC](https://discourse.itk.org/t/best-approach-for-analyzing-microscope-images-with-itk/7799 "2026-09-09T13:03:59Z")
I’m working with microscopy images from lab equipment and want to process/analyze them using ITK. What filters or techniques would you recommend for tasks like cell counting, image segmentation, or noise reduction? Any g… --- ## [Basic questions before contributing](https://discourse.itk.org/t/basic-questions-before-contributing/7797)
**Author:** [@Toddthegod1](https://discourse.itk.org/u/Toddthegod1)\ **Replies:** 1\ **Last updated:** [September 9, 2026, 12:54pm UTC](https://discourse.itk.org/t/basic-questions-before-contributing/7797 "2026-09-09T12:54:25Z")
Hi ITK, I am a senior in college in a course where we have to contribute as a team with other students to an open-source project. Is there anything appropriate I should know before we start to contribute to the project?… --- ## [Different BSpline fixed-parameters for equal-sized images?](https://discourse.itk.org/t/different-bspline-fixed-parameters-for-equal-sized-images/7768)
**Author:** [@reox](https://discourse.itk.org/u/reox)\ **Replies:** 6\ **Last updated:** [June 9, 2026, 6:51am UTC](https://discourse.itk.org/t/different-bspline-fixed-parameters-for-equal-sized-images/7768 "2026-06-09T06:51:07Z")
I started with a very simple registration pipeline, basically like this: import itk fixed\_image = itk.imread('fixed.mhd', itk.F) moving\_image = itk.imread('moving.mhd', itk.F) fixed\_mask = itk.imread("fixed\_mask.mhd",… --- ## [ITK build with TBB](https://discourse.itk.org/t/itk-build-with-tbb/1954)
**Author:** [@nm97](https://discourse.itk.org/u/nm97)\ **Replies:** 23\ **Last updated:** [May 22, 2026, 2:10pm UTC](https://discourse.itk.org/t/itk-build-with-tbb/1954 "2026-05-22T14:10:30Z")
Hi everyone, I am trying to build ITK-5.0.0 with TBB. I have already successfully built TBB. After cmake config I get this error Could not find a package configuration file provided by "TBB" with any of the follow… --- ## [Registation of two vascular images using Python Simple ITK](https://discourse.itk.org/t/registation-of-two-vascular-images-using-python-simple-itk/7766)
**Author:** [@anatolejimenez](https://discourse.itk.org/u/anatolejimenez)\ **Replies:** 1\ **Last updated:** [May 22, 2026, 12:51pm UTC](https://discourse.itk.org/t/registation-of-two-vascular-images-using-python-simple-itk/7766 "2026-05-22T12:51:09Z")
Hi, I would like to register two vascular images of the same modality but with different dynamics. I played a lot with the image registration metrics (correlation, mutual information and correlation) with optimizer grad… --- ## [How to compile the linux target without symlinks?](https://discourse.itk.org/t/how-to-compile-the-linux-target-without-symlinks/7755)
**Author:** [@Rosie](https://discourse.itk.org/u/Rosie)\ **Replies:** 1\ **Last updated:** [April 28, 2026, 10:05am UTC](https://discourse.itk.org/t/how-to-compile-the-linux-target-without-symlinks/7755 "2026-04-28T10:05:02Z")
Dear developers, I would like to compile the linux target of ITK 5.4 by Cmake. It will create symlink binaries (.so and .so.1) which are not supported by windows system. So I wonder if it can be compiled without symlink… --- ## [ITKElastix for Mesh Transformation: TransformixFilter.GetOutputMesh() returns None](https://discourse.itk.org/t/itkelastix-for-mesh-transformation-transformixfilter-getoutputmesh-returns-none/7615)
**Author:** [@DVigneault](https://discourse.itk.org/u/DVigneault)\ **Replies:** 4\ **Last updated:** [April 6, 2026, 1:27pm UTC](https://discourse.itk.org/t/itkelastix-for-mesh-transformation-transformixfilter-getoutputmesh-returns-none/7615 "2026-04-06T13:27:51Z")
All– Say I have used elastix to register a moving image moving.nii.gz to a fixed image fixed.nii.gz, resulting in a transformation file params.txt. I would now like to apply the transformation in params.txt to a mesh i… --- ## [Enable long path compilation](https://discourse.itk.org/t/enable-long-path-compilation/2691)
**Author:** [@Thibault](https://discourse.itk.org/u/Thibault)\ **Replies:** 13\ **Last updated:** [March 5, 2026, 6:30pm UTC](https://discourse.itk.org/t/enable-long-path-compilation/2691 "2026-03-05T18:30:21Z")
Hi, First time here. I was facing the fact that you have deactivated the compilation for long path on windows 10 even if we enabled long path in GPO. See this commit: In your discussion about that issue, I have noti… --- ## [Groupwise registration in SimpleITK or ITKElastix flipping images?](https://discourse.itk.org/t/groupwise-registration-in-simpleitk-or-itkelastix-flipping-images/7694)
**Author:** [@Rock](https://discourse.itk.org/u/Rock)\ **Replies:** 1\ **Last updated:** [January 7, 2026, 7:59pm UTC](https://discourse.itk.org/t/groupwise-registration-in-simpleitk-or-itkelastix-flipping-images/7694 "2026-01-07T19:59:05Z")
Hello, I am trying to run groupwise registrations in SimpleITK and ITKElastix, but with either the resulting images just seem to be flipped vertically. My original images are .tifs; I converted them to grayscale and the… --- ## [Query on Regularization with BSplineTransform and GradientDescent in SimpleITK](https://discourse.itk.org/t/query-on-regularization-with-bsplinetransform-and-gradientdescent-in-simpleitk/7690)
**Author:** [@blue\_sky](https://discourse.itk.org/u/blue_sky)\ **Replies:** 4\ **Last updated:** [January 5, 2026, 4:17pm UTC](https://discourse.itk.org/t/query-on-regularization-with-bsplinetransform-and-gradientdescent-in-simpleitk/7690 "2026-01-05T16:17:06Z")
Hello everyone, I am currently working with SimpleITK for image registration, specifically employing sitk.BSplineTransform and the SetOptimizerAsGradientDescent optimizer. I’ve been reviewing a Python example that demo… --- ## [Different Rotation Matrices between Euler3DTransform and Scipy Rotation](https://discourse.itk.org/t/different-rotation-matrices-between-euler3dtransform-and-scipy-rotation/4273)
**Author:** [@Floowey](https://discourse.itk.org/u/Floowey)\ **Replies:** 6\ **Last updated:** [December 25, 2025, 7:20am UTC](https://discourse.itk.org/t/different-rotation-matrices-between-euler3dtransform-and-scipy-rotation/4273 "2025-12-25T07:20:45Z")
Hello, I’m trying to rotate sections of my images according to certain orientations. However, I noticed some discrepancies between the rotations of the Euler3DTransform object and scipy.spatial.transform.Rotation when g… --- ## [Error MSB8066 during building?](https://discourse.itk.org/t/error-msb8066-during-building/7671)
**Author:** [@Rock](https://discourse.itk.org/u/Rock)\ **Replies:** 7\ **Last updated:** [December 18, 2025, 6:48pm UTC](https://discourse.itk.org/t/error-msb8066-during-building/7671 "2025-12-18T18:48:15Z")
Hello all, I have been trying to get SimpleITK set up with Elastix, following the instructions on the pages for Building SimpleITK and Building SimpleITK on Windows. I am using Visual Studio 18, Python 3.14, and CMake 4… --- ## [Reading/casting .tif images into SimpleITK](https://discourse.itk.org/t/reading-casting-tif-images-into-simpleitk/7683)
**Author:** [@Rock](https://discourse.itk.org/u/Rock)\ **Replies:** 1\ **Last updated:** [December 18, 2025, 5:53pm UTC](https://discourse.itk.org/t/reading-casting-tif-images-into-simpleitk/7683 "2025-12-18T17:53:52Z")
Hello, My lab has .tif images we need to do a groupwise registration on and I am having difficulty reading them into SimpleITK. If I understand correctly, to register images they need to be floats so I have tried readin… --- ## [Error building ITK 5.4 with CMake on MSVC 19.44: unresolved external symbol \_\_std\_find\_first\_of\_trivial\_pos\_1](https://discourse.itk.org/t/error-building-itk-5-4-with-cmake-on-msvc-19-44-unresolved-external-symbol-std-find-first-of-trivial-pos-1/7673)
**Author:** [@thanhst](https://discourse.itk.org/u/thanhst)\ **Replies:** 7\ **Last updated:** [December 1, 2025, 2:02am UTC](https://discourse.itk.org/t/error-building-itk-5-4-with-cmake-on-msvc-19-44-unresolved-external-symbol-std-find-first-of-trivial-pos-1/7673 "2025-12-01T02:02:21Z")
Hi ITK team, I built ITK 5.4 using CMake and Visual Studio 2022. Everything compiles and links fine for most headers, but when I include \ in my project, I get the following linker error with file i… --- ## [itk specified file not found error](https://discourse.itk.org/t/itk-specified-file-not-found-error/7665)
**Author:** [@ali123](https://discourse.itk.org/u/ali123)\ **Replies:** 1\ **Last updated:** [November 17, 2025, 7:12pm UTC](https://discourse.itk.org/t/itk-specified-file-not-found-error/7665 "2025-11-17T19:12:21Z")
hi i,m realy new to c++, vs and itk i install that with vcpkg and integrate install it i add directory lib and include to project property but i still have problem and get this specified file not found can you p… --- ## [Some Dicom format issues](https://discourse.itk.org/t/some-dicom-format-issues/7664)
**Author:** [@Xoz](https://discourse.itk.org/u/Xoz)\ **Replies:** 3\ **Last updated:** [November 15, 2025, 8:34pm UTC](https://discourse.itk.org/t/some-dicom-format-issues/7664 "2025-11-15T20:34:06Z")
Hi everyone, I’ve been working with new @itk-wasm/image-io and @itk-wasm/dicom for a while and met some issues with the file format, some of them may be not in plan to be supported, so I would like to know your opinion … --- ## [Strange output from RegionOfInterestImageFilter](https://discourse.itk.org/t/strange-output-from-regionofinterestimagefilter/7657)
**Author:** [@Vasily\_Postnicov](https://discourse.itk.org/u/Vasily_Postnicov)\ **Replies:** 3\ **Last updated:** [November 6, 2025, 3:14pm UTC](https://discourse.itk.org/t/strange-output-from-regionofinterestimagefilter/7657 "2025-11-06T15:14:38Z")
After applying RegionOfInterestImageFilter to a two-dimensional image like so: #include \ #include \ #include \ #include \ #include… --- ## [Z stack thickness?](https://discourse.itk.org/t/z-stack-thickness/7648)
**Author:** [@PART](https://discourse.itk.org/u/PART)\ **Replies:** 2\ **Last updated:** [October 29, 2025, 1:23pm UTC](https://discourse.itk.org/t/z-stack-thickness/7648 "2025-10-29T13:23:19Z")
Sorry, I’m sure its been asked but I couldn’t find it through the search function but are Z stacks mandatory for multiplexed images registration and if so how does one ensure that you capture the same focal plane with ea… --- ## [Overlaying Structures on CT Images in Axial, Coronal, and Sagittal Views](https://discourse.itk.org/t/overlaying-structures-on-ct-images-in-axial-coronal-and-sagittal-views/7647)
**Author:** [@blue\_sky](https://discourse.itk.org/u/blue_sky)\ **Replies:** 3\ **Last updated:** [October 21, 2025, 1:40pm UTC](https://discourse.itk.org/t/overlaying-structures-on-ct-images-in-axial-coronal-and-sagittal-views/7647 "2025-10-21T13:40:45Z")
Hello everyone, I am working on displaying CT images in the axial, coronal, and sagittal planes, along with dose maps and RTSTRUCT contours. While the CT and dose images are displayed correctly, I am having trouble over… --- ## [The application crashes while generating the NRRD file](https://discourse.itk.org/t/the-application-crashes-while-generating-the-nrrd-file/7646)
**Author:** [@purushothaman\_u](https://discourse.itk.org/u/purushothaman_u)\ **Replies:** 6\ **Last updated:** [October 17, 2025, 1:32pm UTC](https://discourse.itk.org/t/the-application-crashes-while-generating-the-nrrd-file/7646 "2025-10-17T13:32:19Z")
In ticket the below ITK ticket an issue has been reported, I have same DICOM files where Bits allocated is 12 for which an exception is supposed to be raised as mentioned in the ticket’s fix is not working instead my … --- ## [Inappropriate output for rotating a volume using Euler transform in C++](https://discourse.itk.org/t/inappropriate-output-for-rotating-a-volume-using-euler-transform-in-c/7644)
**Author:** [@purushothaman\_u](https://discourse.itk.org/u/purushothaman_u)\ **Replies:** 5\ **Last updated:** [October 11, 2025, 9:51am UTC](https://discourse.itk.org/t/inappropriate-output-for-rotating-a-volume-using-euler-transform-in-c/7644 "2025-10-11T09:51:28Z")
The below code takes the axial volume as input, applies a 90-degree rotation around the z-axis, and writes the output volume to a 90.nrrd file. In 90. When viewing the NRRD file in the ITK-SNAP app, we can see that certa… --- ## [Dice Coefficient Calculation in Python](https://discourse.itk.org/t/dice-coefficient-calculation-in-python/7628)
**Author:** [@blue\_sky](https://discourse.itk.org/u/blue_sky)\ **Replies:** 2\ **Last updated:** [September 11, 2025, 9:01am UTC](https://discourse.itk.org/t/dice-coefficient-calculation-in-python/7628 "2025-09-11T09:01:10Z")
Hello everyone, I’m trying to compute the Dice coefficient using a Python script. To implement this, I have used ideas and code from the following links: “SimpleITK-Notebooks/Python/34\_Segmentation\_Evaluation.ipynb at… --- ## [Registration of CT Images with Large Organ Deformations](https://discourse.itk.org/t/registration-of-ct-images-with-large-organ-deformations/7627)
**Author:** [@blue\_sky](https://discourse.itk.org/u/blue_sky)\ **Replies:** 1\ **Last updated:** [September 2, 2025, 7:49pm UTC](https://discourse.itk.org/t/registration-of-ct-images-with-large-organ-deformations/7627 "2025-09-02T19:49:17Z")
Hello everyone, I have two CT images that I want to register together. One is from external beam radiotherapy (EBRT), and the other is from brachytherapy. Before registration, I harmonized both images by making their Or… --- ## [rtksimulatedgeometry\_ggo.h "verbose\_flag": not "args\_info\_rtksimulatedgeometry" member](https://discourse.itk.org/t/rtksimulatedgeometry-ggo-h-verbose-flag-not-args-info-rtksimulatedgeometry-member/7619)
**Author:** [@ma1282029525](https://discourse.itk.org/u/ma1282029525)\ **Replies:** 2\ **Last updated:** [August 27, 2025, 1:16pm UTC](https://discourse.itk.org/t/rtksimulatedgeometry-ggo-h-verbose-flag-not-args-info-rtksimulatedgeometry-member/7619 "2025-08-27T13:16:12Z")
Is this a compilation bug or a configuration error? I removed the verbose conditional compilation and it passed. --- ## [Unifying CT Images Geometry and Cropping to Common ROI](https://discourse.itk.org/t/unifying-ct-images-geometry-and-cropping-to-common-roi/7614)
**Author:** [@blue\_sky](https://discourse.itk.org/u/blue_sky)\ **Replies:** 3\ **Last updated:** [August 25, 2025, 5:11pm UTC](https://discourse.itk.org/t/unifying-ct-images-geometry-and-cropping-to-common-roi/7614 "2025-08-25T17:11:31Z")
Hi everyone, I am currently working on a medical image processing task that involves the registration of five CT image series for a single patient. My dataset consists of: One CT scan acquired during an External Radiot… --- ## [Limit Number of threads in python SimpleITK programatically](https://discourse.itk.org/t/limit-number-of-threads-in-python-simpleitk-programatically/2723)
**Author:** [@reox](https://discourse.itk.org/u/reox)\ **Replies:** 6\ **Last updated:** [August 13, 2025, 6:44pm UTC](https://discourse.itk.org/t/limit-number-of-threads-in-python-simpleitk-programatically/2723 "2025-08-13T18:44:23Z")
I’m using SimpleITK from python. By default all logical CPUs which are found are used, but I like to constrict this. I already read this thread here: https://discourse.itk.org/t/threading-in-itk/782 and can confirm that … --- ## [Multiple series in a single CT series](https://discourse.itk.org/t/multiple-series-in-a-single-ct-series/1525)
**Author:** [@hadasara](https://discourse.itk.org/u/hadasara)\ **Replies:** 18\ **Last updated:** [July 28, 2025, 6:57pm UTC](https://discourse.itk.org/t/multiple-series-in-a-single-ct-series/1525 "2025-07-28T18:57:53Z")
Hi all, Maybe someone here would know- I came across a CT series, that include 2 series, saved as a single one. When you scroll in axial slices, you see shoulder s to pelvis and then agin shoulders to pelvis in a late… --- ## [MRI-CT phantom registration](https://discourse.itk.org/t/mri-ct-phantom-registration/7598)
**Author:** [@rohit\_inippully](https://discourse.itk.org/u/rohit_inippully)\ **Replies:** 3\ **Last updated:** [July 22, 2025, 1:46pm UTC](https://discourse.itk.org/t/mri-ct-phantom-registration/7598 "2025-07-22T13:46:00Z")
I am trying to register (rigid) a MRI image of a phantom to its CT image. However, I am not getting the results I need. I am using MattesMutual Metric, and regularstepgradient, Euler3DTransform, etc. Has anyone encoun… --- ## [pixi not being found at the expected location at development setup](https://discourse.itk.org/t/pixi-not-being-found-at-the-expected-location-at-development-setup/7589)
**Author:** [@jhlegarreta](https://discourse.itk.org/u/jhlegarreta)\ **Replies:** 4\ **Last updated:** [July 3, 2025, 1:09am UTC](https://discourse.itk.org/t/pixi-not-being-found-at-the-expected-location-at-development-setup/7589 "2025-07-03T01:09:32Z")
Hi, I was trying to set up my local ITK for development on a Windows 10 machine following Contribute to ITK - ITK's documentation. I installed pixi using the MSI provided in their GitHub release page. It turns out tha… [Next page](https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=1)