# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=35

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**Page:** 36

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## [Is there a way to combine two registered images together preserving all the information from non-overlapping parts of both images?](https://discourse.itk.org/t/is-there-a-way-to-combine-two-registered-images-together-preserving-all-the-information-from-non-overlapping-parts-of-both-images/2081)

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**Author:** [@ptolmachev](https://discourse.itk.org/u/ptolmachev)\
**Replies:** 2\
**Last updated:** [July 23, 2019, 6:12am UTC](https://discourse.itk.org/t/is-there-a-way-to-combine-two-registered-images-together-preserving-all-the-information-from-non-overlapping-parts-of-both-images/2081 "2019-07-23T06:12:29Z")

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Hi folks, Suppose, I ve got two 3d images, and after running the registration on them I am able to recover 3d transform which includes shift and rotation. Combining these two images together will give me a union of two …

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## [A question at helloworld](https://discourse.itk.org/t/a-question-at-helloworld/2034)

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**Author:** [@yihongmike](https://discourse.itk.org/u/yihongmike)\
**Replies:** 3\
**Last updated:** [July 21, 2019, 4:15pm UTC](https://discourse.itk.org/t/a-question-at-helloworld/2034 "2019-07-21T16:15:21Z")

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I’m so sorry. It seemed that I have a question when i do it at vs2019. Could someone help me? Thanks!

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## [Linux ITK threads all on same CPU](https://discourse.itk.org/t/linux-itk-threads-all-on-same-cpu/2041)

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**Author:** [@blacava](https://discourse.itk.org/u/blacava)\
**Replies:** 8\
**Last updated:** [July 15, 2019, 10:56pm UTC](https://discourse.itk.org/t/linux-itk-threads-all-on-same-cpu/2041 "2019-07-15T22:56:04Z")

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ITK 4.13.2, Release build On Windows, my ITK app utilizes all 8 CPUs, however on Linux all ITK threads share a single CPU and is dog-slow. If you look at the attached screenshot you’ll see what I mean. BTW: itk::Multi…

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## [itk::ERROR: MeanSampleFilter: Total frequency was too close to zero](https://discourse.itk.org/t/itk-meansamplefilter-total-frequency-was-too-close-to-zero/1989)

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**Author:** [@ine](https://discourse.itk.org/u/ine)\
**Replies:** 7\
**Last updated:** [July 15, 2019, 9:39am UTC](https://discourse.itk.org/t/itk-meansamplefilter-total-frequency-was-too-close-to-zero/1989 "2019-07-15T09:39:51Z")

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Hello, I’m quite new to C++ and ITK (I have mainly used Python and SimpleITK up until now). I’m trying to read an image and get some statistics from this image, but only in an ellipse-shaped region. For this, I am usi…

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## [sitk.ReadImage for known deformation fields in dcm](https://discourse.itk.org/t/sitk-readimage-for-known-deformation-fields-in-dcm/1093)

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**Author:** [@JuanC](https://discourse.itk.org/u/JuanC)\
**Replies:** 2\
**Last updated:** [July 15, 2019, 9:23am UTC](https://discourse.itk.org/t/sitk-readimage-for-known-deformation-fields-in-dcm/1093 "2019-07-15T09:23:31Z")

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Hi all, I have a deformation field calculated by a different software in dcm format and I want to import it using simpleITK. When I use: dis = sitk.ReadImage(‘dvf.dcm’, sitk.sitkVectorFloat64) Throws the error: Runt…

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## [Distorted DICOM import on Slicer](https://discourse.itk.org/t/distorted-dicom-import-on-slicer/2043)

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**Author:** [@Amine](https://discourse.itk.org/u/Amine)\
**Replies:** 0\
**Last updated:** [July 15, 2019, 12:39am UTC](https://discourse.itk.org/t/distorted-dicom-import-on-slicer/2043 "2019-07-15T00:39:45Z")

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Hi, coming from 3D Slicer Forum, i was advised to post this issue here There is a link to the original thread with more info: DICOM file: https://drive.google.com/drive/folders/1RgqhZjg6hXBfXKWZYmBYJOfFyq\_XxxiS Th…

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## [Build HelloWorld error](https://discourse.itk.org/t/build-helloworld-error/1873)

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**Author:** [@yinpeter](https://discourse.itk.org/u/yinpeter)\
**Replies:** 19\
**Last updated:** [July 13, 2019, 2:10am UTC](https://discourse.itk.org/t/build-helloworld-error/1873 "2019-07-13T02:10:27Z")

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Build Env.: MacOS: 10.13.6 Xcode: 10.1 ITK: ITK 5.0 Release Candidate 2 Error: ! Apple Mach-O Linder(id) Error !Linker command failed with exit code 1(use -v to see invocation) detail: ld: library not found for -…

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## [Reading DICOM-RT tags](https://discourse.itk.org/t/reading-dicom-rt-tags/2038)

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**Author:** [@Gabriele\_Belotti](https://discourse.itk.org/u/Gabriele_Belotti)\
**Replies:** 5\
**Last updated:** [July 12, 2019, 12:25pm UTC](https://discourse.itk.org/t/reading-dicom-rt-tags/2038 "2019-07-12T12:25:44Z")

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Hi everyone, I am trying to automatically extract tags from an RT file, however ITK doesn’t directly support this kind of format. I really don’t need to extract/use the contours, I just need to find the information con…

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## [How to set parameters on CED, EED and cCEED](https://discourse.itk.org/t/how-to-set-parameters-on-ced-eed-and-cceed/2030)

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**Author:** [@Dimitris\_Lolis](https://discourse.itk.org/u/Dimitris_Lolis)\
**Replies:** 6\
**Last updated:** [July 11, 2019, 10:33am UTC](https://discourse.itk.org/t/how-to-set-parameters-on-ced-eed-and-cceed/2030 "2019-07-11T10:33:34Z")

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Hello, I’m quite new to this framework but i can’t get a grasp of how to use its python interface. I would like to replicate the weikert Diffusion type in the simplest way possible by denoising some of my own images lik…

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## [“exception occurred during imageIO”](https://discourse.itk.org/t/exception-occurred-during-imageio/2016)

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**Author:** [@jeroch](https://discourse.itk.org/u/jeroch)\
**Replies:** 4\
**Last updated:** [July 10, 2019, 5:24am UTC](https://discourse.itk.org/t/exception-occurred-during-imageio/2016 "2019-07-10T05:24:03Z")

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hello sir ,when I save edited image used format .mha in macOS, one exception occurred like that. How to solve the question?

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## [Line structuring element in any orientations](https://discourse.itk.org/t/line-structuring-element-in-any-orientations/2004)

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**Author:** [@Jonas](https://discourse.itk.org/u/Jonas)\
**Replies:** 5\
**Last updated:** [July 9, 2019, 3:27am UTC](https://discourse.itk.org/t/line-structuring-element-in-any-orientations/2004 "2019-07-09T03:27:02Z")

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Hello, I’m trying to implement “The Multiscale Bowler-Hat Transform for Vessel Enhancement in 3D Biomedical Images” by creating a custom itk filter. They use morphological grayscale openings with a combination of spher…

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## [Read mha metadata](https://discourse.itk.org/t/read-mha-metadata/2007)

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**Author:** [@Gabriele\_Belotti](https://discourse.itk.org/u/Gabriele_Belotti)\
**Replies:** 15\
**Last updated:** [July 8, 2019, 8:58am UTC](https://discourse.itk.org/t/read-mha-metadata/2007 "2019-07-08T08:58:34Z")

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Hi everyone, I’m trying to extract information about a volume which is in .mha format. I’m struggling to find examples on how to read metadata of images which aren’t DICOM and I would like to automatically extract info…

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## [Correct way to interrupt processing with AbortGenerateData](https://discourse.itk.org/t/correct-way-to-interrupt-processing-with-abortgeneratedata/2006)

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**Author:** [@IanL](https://discourse.itk.org/u/IanL)\
**Replies:** 3\
**Last updated:** [July 4, 2019, 11:17am UTC](https://discourse.itk.org/t/correct-way-to-interrupt-processing-with-abortgeneratedata/2006 "2019-07-04T11:17:46Z")

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Hi all, I am trying to determine the correct way to interrupt processing of a segmentation pipeline. This will be from a user request, application shutdown, etc. The segmentation is running in a worker thread and the ca…

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## [Using cmake to build SimpleITK](https://discourse.itk.org/t/using-cmake-to-build-simpleitk/373)

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**Author:** [@Pythonsegmenter](https://discourse.itk.org/u/Pythonsegmenter)\
**Replies:** 21\
**Last updated:** [July 2, 2019, 12:21pm UTC](https://discourse.itk.org/t/using-cmake-to-build-simpleitk/373 "2019-07-02T12:21:29Z")

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Hi guys, So i followed the tutorial I found here: http://simpleitk.readthedocs.io/en/master/Documentation/docs/source/building.html#recipes-formulas-short-cuts to build the latest unreleased SimpleITK version. I downlo…

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## [TwoProjectionRegistration - 2D 3D registration](https://discourse.itk.org/t/twoprojectionregistration-2d-3d-registration/1972)

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**Author:** [@Gabriele\_Belotti](https://discourse.itk.org/u/Gabriele_Belotti)\
**Replies:** 2\
**Last updated:** [June 30, 2019, 3:29pm UTC](https://discourse.itk.org/t/twoprojectionregistration-2d-3d-registration/1972 "2019-06-30T15:29:14Z")

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Dear all, I’m testing this particular module to evaluate a 2D/3D registration context. I was able to obtain DRRs using Siddon-Jacobs ray tracing method (starting point is an FDK of POPI model) and as a proof of concept…

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## [Voxel membership tests and contours from meshes](https://discourse.itk.org/t/voxel-membership-tests-and-contours-from-meshes/1993)

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**Author:** [@danelliottster](https://discourse.itk.org/u/danelliottster)\
**Replies:** 1\
**Last updated:** [June 25, 2019, 4:57pm UTC](https://discourse.itk.org/t/voxel-membership-tests-and-contours-from-meshes/1993 "2019-06-25T16:57:28Z")

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I am investigating whether or not we can convert a signification portion of our software to ITK. I’ve written a sample program to do much of what we need but there is still a couple significant question marks. I’ve don…

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## [Simpleitk gui.py not showing sliders](https://discourse.itk.org/t/simpleitk-gui-py-not-showing-sliders/1968)

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**Author:** [@nsp8](https://discourse.itk.org/u/nsp8)\
**Replies:** 2\
**Last updated:** [June 17, 2019, 3:32pm UTC](https://discourse.itk.org/t/simpleitk-gui-py-not-showing-sliders/1968 "2019-06-17T15:32:56Z")

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Hi all, Does anyone know why the slider not showing up in jupyter notebook when i try to display 3d images using the gui.MultiImageDisplay function? I just got a view of one slice. The code: gui.MultiImageDisplay(\[im1…

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## [ITKFFTExport.h is missing?](https://discourse.itk.org/t/itkfftexport-h-is-missing/1966)

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**Author:** [@revolvet](https://discourse.itk.org/u/revolvet)\
**Replies:** 4\
**Last updated:** [June 14, 2019, 3:50pm UTC](https://discourse.itk.org/t/itkfftexport-h-is-missing/1966 "2019-06-14T15:50:54Z")

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Hi. I’m trying to build python wrapper for ITK. There is an error saying that MSVC 16.1.2 (2019) (Windows 10) can’t find ITKFFTExport.h. I search through the source folder and can’t find this header. itkFFTWGlobalConfigu…

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## [iterative inverse displacement filter in ITK](https://discourse.itk.org/t/iterative-inverse-displacement-filter-in-itk/1952)

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**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 8\
**Last updated:** [June 13, 2019, 12:34pm UTC](https://discourse.itk.org/t/iterative-inverse-displacement-filter-in-itk/1952 "2019-06-13T12:34:09Z")

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Are there any examples (code) where this filter is used?

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## [simpleitk.show not returning handles after execution](https://discourse.itk.org/t/simpleitk-show-not-returning-handles-after-execution/1962)

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**Author:** [@nsp8](https://discourse.itk.org/u/nsp8)\
**Replies:** 1\
**Last updated:** [June 12, 2019, 6:54pm UTC](https://discourse.itk.org/t/simpleitk-show-not-returning-handles-after-execution/1962 "2019-06-12T18:54:26Z")

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Hi all, When I try to sitk.show(img), an imageJ windows pop up with the image I want to show. But inside the jupyter notebook, it still shows busy kernel even after close the imagej window. Does anyone know why this hap…

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## [GDCM not found when ITK 5.0 is installed as shared library](https://discourse.itk.org/t/gdcm-not-found-when-itk-5-0-is-installed-as-shared-library/1955)

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**Author:** [@lukas](https://discourse.itk.org/u/lukas)\
**Replies:** 0\
**Last updated:** [June 10, 2019, 12:02pm UTC](https://discourse.itk.org/t/gdcm-not-found-when-itk-5-0-is-installed-as-shared-library/1955 "2019-06-10T12:02:22Z")

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Hi all, When trying to run an application built with ITK 5.0 installed as a shared library, I get the error: error while loading shared libraries: libitkgdcmjpeg8-5.0.so.1: cannot open shared object file: No such file…

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## [ITK 5.0 DeformableRegistration15.cxx](https://discourse.itk.org/t/itk-5-0-deformableregistration15-cxx/1948)

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**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 1\
**Last updated:** [June 6, 2019, 6:45pm UTC](https://discourse.itk.org/t/itk-5-0-deformableregistration15-cxx/1948 "2019-06-06T18:45:21Z")

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Im not able to build this file in Visual Studio 2109. the following error arises. Please help me fix this issue 1\>------ Build started: Project: itkv3p\_netlib, Configuration: Debug x64 ------ 2\>------ Build started: Pr…

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## [ITK - Concept checking error](https://discourse.itk.org/t/itk-concept-checking-error/1946)

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**Author:** [@Pooja\_Virkar](https://discourse.itk.org/u/Pooja_Virkar)\
**Replies:** 1\
**Last updated:** [June 5, 2019, 2:26pm UTC](https://discourse.itk.org/t/itk-concept-checking-error/1946 "2019-06-05T14:26:50Z")

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Hello, I am trying to segment tumour in liver. I made one program which is working fine with 2D images. but when I am trying to run 3D series for the same program, its showing following “Concept checking” error. /us…

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## ["This stuff is hard!" resources to start learning about registration](https://discourse.itk.org/t/this-stuff-is-hard-resources-to-start-learning-about-registration/1886)

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**Author:** [@vzickus](https://discourse.itk.org/u/vzickus)\
**Replies:** 10\
**Last updated:** [June 3, 2019, 11:36am UTC](https://discourse.itk.org/t/this-stuff-is-hard-resources-to-start-learning-about-registration/1886 "2019-06-03T11:36:32Z")

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Hi everyone, I have been playing around with “turning the knobs” for registration for some time now, but I feel most of the time it is still a black-box to me. I wonder if I lack a good foundation for image registration…

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## [Data Augmentation of 3d medical images using SimpleITK](https://discourse.itk.org/t/data-augmentation-of-3d-medical-images-using-simpleitk/1935)

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**Author:** [@jayant\_prakash](https://discourse.itk.org/u/jayant_prakash)\
**Replies:** 1\
**Last updated:** [June 2, 2019, 12:15am UTC](https://discourse.itk.org/t/data-augmentation-of-3d-medical-images-using-simpleitk/1935 "2019-06-02T00:15:18Z")

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Hello everyone, I am new to this amazing library. I am working on classification of lymph nodes using deep learning, therefore, I need to do data augmentation of 3D ROIs (of shape 32X32X32) like 3d rotation, 3d translat…

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## [itk doesn't work with c++17](https://discourse.itk.org/t/itk-doesnt-work-with-c-17/1911)

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**Author:** [@eninyo](https://discourse.itk.org/u/eninyo)\
**Replies:** 3\
**Last updated:** [May 27, 2019, 2:04pm UTC](https://discourse.itk.org/t/itk-doesnt-work-with-c-17/1911 "2019-05-27T14:04:00Z")

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hello, i’m using the itkImageAlgorithm H file and i get the following error: itkImageAlgorithm.h:193: error: C2143: syntax error: missing ‘,’ before ‘\<’ this is the code: /\*\* Unary functor just for static\_cast operat…

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## [How to save the deformation field ?](https://discourse.itk.org/t/how-to-save-the-deformation-field/1910)

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**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 4\
**Last updated:** [May 25, 2019, 11:47am UTC](https://discourse.itk.org/t/how-to-save-the-deformation-field/1910 "2019-05-25T11:47:26Z")

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I am executing deformableregistration15.cxx I wonder how to save the deformation field? In which format should I save it? It didn’t happen with both mhd and mha formats.

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## [How to deal with HoughTransform2DLinesImageFilter GetLines() method in python](https://discourse.itk.org/t/how-to-deal-with-houghtransform2dlinesimagefilter-getlines-method-in-python/1861)

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**Author:** [@nick](https://discourse.itk.org/u/nick)\
**Replies:** 24\
**Last updated:** [May 24, 2019, 1:37pm UTC](https://discourse.itk.org/t/how-to-deal-with-houghtransform2dlinesimagefilter-getlines-method-in-python/1861 "2019-05-24T13:37:16Z")

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Dear All, I’m trying to use HoughTransform2DLinesImageFilter in python. However, I cannot understand how to use the output of the GetLines() method. AFAIU, the filter should return a list o the lines detected: how do …

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## [Support for ECG](https://discourse.itk.org/t/support-for-ecg/1909)

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**Author:** [@zubair.khan](https://discourse.itk.org/u/zubair.khan)\
**Replies:** 0\
**Last updated:** [May 24, 2019, 7:07am UTC](https://discourse.itk.org/t/support-for-ecg/1909 "2019-05-24T07:07:12Z")

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Hi, Does Dcmtk support ECG? Does anyone have any examples to show how we are supposed to add data to plot the ECG?

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## [Unable to keep image origin and orientation with Python ITK](https://discourse.itk.org/t/unable-to-keep-image-origin-and-orientation-with-python-itk/1907)

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**Author:** [@pfreire](https://discourse.itk.org/u/pfreire)\
**Replies:** 4\
**Last updated:** [May 23, 2019, 6:22pm UTC](https://discourse.itk.org/t/unable-to-keep-image-origin-and-orientation-with-python-itk/1907 "2019-05-23T18:22:15Z")

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Hello, everyone. I’m trying to perform a very simple operation on an image using Python. I just want to read it as a NumPy array, change some values and then write it back as a new image. The problem is: when I write it…

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