# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=33

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**Page:** 34

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## [fast marching question](https://discourse.itk.org/t/fast-marching-question/2461)

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**Author:** [@kayarre](https://discourse.itk.org/u/kayarre)\
**Replies:** 0\
**Last updated:** [November 29, 2019, 1:59pm UTC](https://discourse.itk.org/t/fast-marching-question/2461 "2019-11-29T13:59:13Z")

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Hi, I am attempting to remove part of the background of an image as it causes issues with the registration pipeline (i think). I am using a combination of FastMarchingUpwindGradientImageFilter and ScalarChanAndVeseDense…

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## [Is there any filter replaced the itkdifferenceimagefilter in ITK4.5?](https://discourse.itk.org/t/is-there-any-filter-replaced-the-itkdifferenceimagefilter-in-itk4-5/2454)

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**Author:** [@Ranglage](https://discourse.itk.org/u/Ranglage)\
**Replies:** 1\
**Last updated:** [November 27, 2019, 2:23pm UTC](https://discourse.itk.org/t/is-there-any-filter-replaced-the-itkdifferenceimagefilter-in-itk4-5/2454 "2019-11-27T14:23:05Z")

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Since the itkdifferenceimagefilter has removed from ITK5.0. Is there any filter replaced the itkdifferenceimagefilter from ITK4.5?

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## [How to create vtkUnstructuredGrid from an itk::Image?](https://discourse.itk.org/t/how-to-create-vtkunstructuredgrid-from-an-itk-image/2364)

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**Author:** [@Sara\_Caffe](https://discourse.itk.org/u/Sara_Caffe)\
**Replies:** 11\
**Last updated:** [November 26, 2019, 12:53pm UTC](https://discourse.itk.org/t/how-to-create-vtkunstructuredgrid-from-an-itk-image/2364 "2019-11-26T12:53:47Z")

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Hi, I have binary label files in itk::Image. I have gone through a few examples in ITK and VTK. What I understood, we need to create the cell type object for generating a specific mesh in both ITK and Vtk. For example, …

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## [capture stdout](https://discourse.itk.org/t/capture-stdout/2431)

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**Author:** [@kayarre](https://discourse.itk.org/u/kayarre)\
**Replies:** 1\
**Last updated:** [November 21, 2019, 3:08am UTC](https://discourse.itk.org/t/capture-stdout/2431 "2019-11-21T03:08:44Z")

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I would like to capture stdout for a portion of a command that doesn’t have a direct python interface. e.g. SimpleElastix has this command sitk.PrintParameterMap(rigid) but I would like to parse the stdout, but I Don’…

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## [IsolatedConnectedImageFilter](https://discourse.itk.org/t/isolatedconnectedimagefilter/2429)

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**Author:** [@abir](https://discourse.itk.org/u/abir)\
**Replies:** 1\
**Last updated:** [November 20, 2019, 8:15pm UTC](https://discourse.itk.org/t/isolatedconnectedimagefilter/2429 "2019-11-20T20:15:37Z")

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I have been working on an exemple of segmentation, for this exemple a threshold must be provided :: isolatedConnected-\>SetLower( lowerThreshold ) So can any one give me an idea how can I specify this threshold for my…

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## [Metric to evaluate the registration accuracy on 3D MRI](https://discourse.itk.org/t/metric-to-evaluate-the-registration-accuracy-on-3d-mri/2426)

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**Author:** [@thanhduc1910](https://discourse.itk.org/u/thanhduc1910)\
**Replies:** 2\
**Last updated:** [November 20, 2019, 2:08pm UTC](https://discourse.itk.org/t/metric-to-evaluate-the-registration-accuracy-on-3d-mri/2426 "2019-11-20T14:08:56Z")

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Hello, I am a newbie to ITK registration. Currently, I am implementing intra-subject registration of 3D PET (moving image) into 3D MRI (fixed image) using ITK. I want to check the registration accuracy which is the erro…

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## [Extracting Exact Metric Value in SimpleITK Python](https://discourse.itk.org/t/extracting-exact-metric-value-in-simpleitk-python/2423)

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**Author:** [@jhess](https://discourse.itk.org/u/jhess)\
**Replies:** 6\
**Last updated:** [November 19, 2019, 5:57pm UTC](https://discourse.itk.org/t/extracting-exact-metric-value-in-simpleitk-python/2423 "2019-11-19T17:57:47Z")

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Hi there, I am using Elastix in command line to register images using Mattes mutual information metric, and at the end of the registration process, I am recording the exact metric value between the fixed and moving imag…

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## [ImageToVTKImageFilter](https://discourse.itk.org/t/imagetovtkimagefilter/2409)

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**Author:** [@nour](https://discourse.itk.org/u/nour)\
**Replies:** 1\
**Last updated:** [November 15, 2019, 10:29pm UTC](https://discourse.itk.org/t/imagetovtkimagefilter/2409 "2019-11-15T22:29:28Z")

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Hi, I am working with MRI database with Nifti format (.nii.gz) and I need to convert them to meshes (.vtk) I am building from sources and install to the system site-packages directory.(ITK and VTK) But I have some trou…

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## [PyInstaller with ITK Python wrapping built from source](https://discourse.itk.org/t/pyinstaller-with-itk-python-wrapping-built-from-source/2411)

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**Author:** [@Aisec](https://discourse.itk.org/u/Aisec)\
**Replies:** 1\
**Last updated:** [November 15, 2019, 12:29pm UTC](https://discourse.itk.org/t/pyinstaller-with-itk-python-wrapping-built-from-source/2411 "2019-11-15T12:29:24Z")

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Hello, I need to create windows 7 binaries of Python application that uses ITK, both 64 and 32 bit versions. I successfully created 64 bit version with itk installed using pip and using this hook file, which i found som…

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## [Issue VS2019 ITK build](https://discourse.itk.org/t/issue-vs2019-itk-build/2385)

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**Author:** [@fraca](https://discourse.itk.org/u/fraca)\
**Replies:** 3\
**Last updated:** [November 7, 2019, 1:23pm UTC](https://discourse.itk.org/t/issue-vs2019-itk-build/2385 "2019-11-07T13:23:38Z")

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I tried to build in Visual Studio 2019 (after processing 5.0.1 Toolkit in CMake) ALL\_BUILD, but 5 process (of 245) have not been completed. Can you help me? It says: “Call API PDB failed. Code error:3” and the last er…

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## [\[SOLVED\] Undefined reference to QuickView even with ITKVtkGlue added in target\_link\_libraries](https://discourse.itk.org/t/solved-undefined-reference-to-quickview-even-with-itkvtkglue-added-in-target-link-libraries/1100)

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**Author:** [@federico](https://discourse.itk.org/u/federico)\
**Replies:** 8\
**Last updated:** [November 7, 2019, 3:58am UTC](https://discourse.itk.org/t/solved-undefined-reference-to-quickview-even-with-itkvtkglue-added-in-target-link-libraries/1100 "2019-11-07T03:58:31Z")

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Hi, I am trying to open and display an image with QuickView, however the linker is unable to find QuickView::AddImage. CMakeFiles/viewer.dir/viewer.cc.o: In function \`main': viewer.cc:(.text+0x12d): undefined reference…

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## [Geodesic active contour with python](https://discourse.itk.org/t/geodesic-active-contour-with-python/2386)

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**Author:** [@abir](https://discourse.itk.org/u/abir)\
**Replies:** 3\
**Last updated:** [November 6, 2019, 9:39pm UTC](https://discourse.itk.org/t/geodesic-active-contour-with-python/2386 "2019-11-06T21:39:23Z")

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i tried to implement the GeodesicActiveContourImageFilter but every time i try to run it i get this message

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## [How to set FixedInitialTransform in itk::MultiResolutionImageRegistrationMethod](https://discourse.itk.org/t/how-to-set-fixedinitialtransform-in-itk-multiresolutionimageregistrationmethod/2377)

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**Author:** [@fangc](https://discourse.itk.org/u/fangc)\
**Replies:** 3\
**Last updated:** [November 5, 2019, 4:22pm UTC](https://discourse.itk.org/t/how-to-set-fixedinitialtransform-in-itk-multiresolutionimageregistrationmethod/2377 "2019-11-05T16:22:16Z")

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Hello, I am using ITK to build my own multi-resolution rigid registration of 3D images. I want to pass the initial transforms of the fixed image and the moving image to the registration. How to do it? Here is my code. …

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## [How to save my medical images in various formats into .zraw?](https://discourse.itk.org/t/how-to-save-my-medical-images-in-various-formats-into-zraw/2371)

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**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 1\
**Last updated:** [November 4, 2019, 5:08am UTC](https://discourse.itk.org/t/how-to-save-my-medical-images-in-various-formats-into-zraw/2371 "2019-11-04T05:08:28Z")

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I mean how to compress my image volume data which is in .mhd into .zraw ? I tried using Convert3D GUI. but .zraw is not possible with it.

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## [How to changes the values of itk::Image?](https://discourse.itk.org/t/how-to-changes-the-values-of-itk-image/2356)

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**Author:** [@Sara\_Caffe](https://discourse.itk.org/u/Sara_Caffe)\
**Replies:** 2\
**Last updated:** [October 30, 2019, 5:42am UTC](https://discourse.itk.org/t/how-to-changes-the-values-of-itk-image/2356 "2019-10-30T05:42:12Z")

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I have the ground truth label files with integer values. I need to remove all values except those voxels that have value==1. How can I do this? How to know the unique values of itk::Image type? Sorry for basic question …

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## [BinaryDilateImageFilterType slow speed. Other option?](https://discourse.itk.org/t/binarydilateimagefiltertype-slow-speed-other-option/2362)

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**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 3\
**Last updated:** [October 29, 2019, 4:57pm UTC](https://discourse.itk.org/t/binarydilateimagefiltertype-slow-speed-other-option/2362 "2019-10-29T16:57:35Z")

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Hi everybody, I need to use the BinaryDilateImageFilterType up to 100 of radii to close gaps but i found it really slow, i wonder if there is another fitlter to do the same with a better speed, more optimized?. Thank y…

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## [itk for Python 3.8](https://discourse.itk.org/t/itk-for-python-3-8/2346)

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**Author:** [@alkamid](https://discourse.itk.org/u/alkamid)\
**Replies:** 2\
**Last updated:** [October 28, 2019, 4:00pm UTC](https://discourse.itk.org/t/itk-for-python-3-8/2346 "2019-10-28T16:00:07Z")

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When can we expect a Python 3.8 version of itk on PyPI? It looks like SimpleITK wheels for 3.8 have already been uploaded.

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## [Deform Registration 3D example 7 BSpline](https://discourse.itk.org/t/deform-registration-3d-example-7-bspline/2344)

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**Author:** [@banikr](https://discourse.itk.org/u/banikr)\
**Replies:** 2\
**Last updated:** [October 24, 2019, 3:02pm UTC](https://discourse.itk.org/t/deform-registration-3d-example-7-bspline/2344 "2019-10-24T15:02:26Z")

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Hello, I was trying to implement deform registration from example7 : https://itk.org/Doxygen/html/Examples\_2RegistrationITKv4\_2DeformableRegistration7\_8cxx-example.html //Deformable registration using BSpline Transform…

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## [Beginner in ITK, Averaging Image](https://discourse.itk.org/t/beginner-in-itk-averaging-image/2328)

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**Author:** [@banikr](https://discourse.itk.org/u/banikr)\
**Replies:** 6\
**Last updated:** [October 21, 2019, 5:11pm UTC](https://discourse.itk.org/t/beginner-in-itk-averaging-image/2328 "2019-10-21T17:11:09Z")

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Hello all, I am new in ITK and using it with CMAKE, GCC compiler. As a python/Matlab programmer, I am finding ITK a bit confusing. But I am trying to do a project that will help me to learn ITK in general. I find the pr…

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## [itk::image to itk::vector](https://discourse.itk.org/t/itk-image-to-itk-vector/2335)

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**Author:** [@kdavis63](https://discourse.itk.org/u/kdavis63)\
**Replies:** 1\
**Last updated:** [October 21, 2019, 3:55pm UTC](https://discourse.itk.org/t/itk-image-to-itk-vector/2335 "2019-10-21T15:55:56Z")

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Sorry if I am missing something in the documentation, but after two days I feel completely at a loss. I am trying to do a transform on an itk::image. Specifically a FixedCenterOfRotationAffineTransform, basically a rotat…

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## [difference open image with pydicom or sitk](https://discourse.itk.org/t/difference-open-image-with-pydicom-or-sitk/2332)

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**Author:** [@stag-phys](https://discourse.itk.org/u/stag-phys)\
**Replies:** 3\
**Last updated:** [October 18, 2019, 4:19pm UTC](https://discourse.itk.org/t/difference-open-image-with-pydicom-or-sitk/2332 "2019-10-18T16:19:09Z")

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Hello everybody, I tried to open a DICOM image with sitk.ReadImage. I don’t have any error message, so I can see the image with plt.imshow, but all the pixels of the image are equal to 0. If I try to open the same imag…

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## [Unable to write dicom file with double values](https://discourse.itk.org/t/unable-to-write-dicom-file-with-double-values/2299)

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**Author:** [@Hasna\_R](https://discourse.itk.org/u/Hasna_R)\
**Replies:** 9\
**Last updated:** [October 9, 2019, 10:23am UTC](https://discourse.itk.org/t/unable-to-write-dicom-file-with-double-values/2299 "2019-10-09T10:23:33Z")

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Hi, I set pixel value of image with double value and tried to save image as dicom file. I am getting error like this “Description: itk::ERROR: GDCMImageIO(0573B7B0): A Floating point buffer was passed but the stored pi…

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## [Unable to update header tags and save dicom file](https://discourse.itk.org/t/unable-to-update-header-tags-and-save-dicom-file/2313)

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**Author:** [@Hasna\_R](https://discourse.itk.org/u/Hasna_R)\
**Replies:** 0\
**Last updated:** [October 9, 2019, 7:26am UTC](https://discourse.itk.org/t/unable-to-update-header-tags-and-save-dicom-file/2313 "2019-10-09T07:26:58Z")

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Hi, I am trying to create an image ,update some tags and save image as dicom file. If i set Meta Data Dictionary to image , writer is throwing an exception. Below is the code typedef itk::Image\<signed short , 2 \> Im…

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## [ITK Python Quick Start Guide updated for ITK 5.0](https://discourse.itk.org/t/itk-python-quick-start-guide-updated-for-itk-5-0/2301)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 0\
**Last updated:** [October 4, 2019, 6:33pm UTC](https://discourse.itk.org/t/itk-python-quick-start-guide-updated-for-itk-5-0/2301 "2019-10-04T18:33:49Z")

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The ITK Python Quick Start Guide has been updated for ITK 5.0! :tada: From basic examples, e.g.: import itk import sys input\_filename = sys.argv\[1\] output\_filename = sys.argv\[2\] image = itk.imread(input\_filename) me…

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## [How to pass a specific label to LabelOverlapMeasuresImageFilter](https://discourse.itk.org/t/how-to-pass-a-specific-label-to-labeloverlapmeasuresimagefilter/2300)

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**Author:** [@TanjaIvanovska](https://discourse.itk.org/u/TanjaIvanovska)\
**Replies:** 1\
**Last updated:** [October 4, 2019, 6:16pm UTC](https://discourse.itk.org/t/how-to-pass-a-specific-label-to-labeloverlapmeasuresimagefilter/2300 "2019-10-04T18:16:01Z")

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Hi, i would like to get values of the overlap measures for specific labels in my masks, and not just the averaged values for all mask labels. In the original code of Nick Tustison that was possible, but i do not find h…

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## [read and render transformed DICOM image from 3D slicer](https://discourse.itk.org/t/read-and-render-transformed-dicom-image-from-3d-slicer/2291)

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**Author:** [@TY\_Park](https://discourse.itk.org/u/TY_Park)\
**Replies:** 5\
**Last updated:** [October 4, 2019, 2:19am UTC](https://discourse.itk.org/t/read-and-render-transformed-dicom-image-from-3d-slicer/2291 "2019-10-04T02:19:24Z")

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I have the 2 DICOM images (MRI and CT) And I performed rigid registration between MRI and CT (the CT was transformed) in “3D Slicer” Then I would like to do volume rendering use transformed CT image However, the trans…

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## [CellPicker example glitch](https://discourse.itk.org/t/cellpicker-example-glitch/2295)

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**Author:** [@EmileSonneveld](https://discourse.itk.org/u/EmileSonneveld)\
**Replies:** 2\
**Last updated:** [October 2, 2019, 3:46pm UTC](https://discourse.itk.org/t/cellpicker-example-glitch/2295 "2019-10-02T15:46:09Z")

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Hi, In the following example there seem to have a glitch: https://kitware.github.io/vtk-js/examples/CellPicker.html Some points are considered to be on the Cell, while actually they appear in mid air. Is this intentio…

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## [CentOS: ITKConfig.cmake not found](https://discourse.itk.org/t/centos-itkconfig-cmake-not-found/2275)

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**Author:** [@OtagoHarbour](https://discourse.itk.org/u/OtagoHarbour)\
**Replies:** 4\
**Last updated:** [October 2, 2019, 1:11pm UTC](https://discourse.itk.org/t/centos-itkconfig-cmake-not-found/2275 "2019-10-02T13:11:25Z")

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I am using CentOS 7.6.1810 and have just installed itk and vtk using sudo yum localinstall InsightToolkit-4.9.1-1.sdl6.i686.rpm and sudo yum localinstall vtk-6.1.0-5.sdl7.x86\_64.rpm respectively. Both ran to complet…

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## [specifying bones by lines](https://discourse.itk.org/t/specifying-bones-by-lines/2289)

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**Author:** [@epilicer](https://discourse.itk.org/u/epilicer)\
**Replies:** 2\
**Last updated:** [October 2, 2019, 12:34am UTC](https://discourse.itk.org/t/specifying-bones-by-lines/2289 "2019-10-02T00:34:34Z")

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Hi, I am a physicist and have recently started to orient in data science. I came an idea to calculate the angle for the valgus deformation from an x-ray image (attachment). All I did for the moment is to read image and …

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## [Image Registration (3D volume)](https://discourse.itk.org/t/image-registration-3d-volume/2278)

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**Author:** [@maiada](https://discourse.itk.org/u/maiada)\
**Replies:** 1\
**Last updated:** [September 30, 2019, 2:25pm UTC](https://discourse.itk.org/t/image-registration-3d-volume/2278 "2019-09-30T14:25:00Z")

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i’m new in ITK and i’m asked to write image registration function in c++ similar to the one used in MATLAB (intensity-based) , by making intensity-based image registration between couple of 3D volumes Optimizer type is…

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