# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=39

[Latest](https://discourse.itk.org/latest.md) · [Categories](https://discourse.itk.org/categories.md) · [Tags](https://discourse.itk.org/tags.md)

**Page:** 40

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## [Problem linking SimpleITK with ImageJ](https://discourse.itk.org/t/problem-linking-simpleitk-with-imagej/1156)

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**Author:** [@tia](https://discourse.itk.org/u/tia)\
**Replies:** 8\
**Last updated:** [August 3, 2018, 11:51pm UTC](https://discourse.itk.org/t/problem-linking-simpleitk-with-imagej/1156 "2018-08-03T23:51:33Z")

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Hello, I apologize in advance for such an elementary question but I am having a surprising amount of trouble getting SimpleITK to open ImageJ as a viewer. I have installed python on my Windows 7 work computer using Ana…

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## [Using SimpleITK for stitching medical volumes with overlap](https://discourse.itk.org/t/using-simpleitk-for-stitching-medical-volumes-with-overlap/1174)

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**Author:** [@malekosh](https://discourse.itk.org/u/malekosh)\
**Replies:** 1\
**Last updated:** [August 2, 2018, 1:31pm UTC](https://discourse.itk.org/t/using-simpleitk-for-stitching-medical-volumes-with-overlap/1174 "2018-08-02T13:31:52Z")

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Hello All, I am trying to stitch 2 MRI scans which have a region of overlap by first registering them together using Elastix Image Filter. Then in order to add (stitch) them together I have to align them both on the sam…

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## [LineIterator](https://discourse.itk.org/t/lineiterator/1170)

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**Author:** [@crossmanith](https://discourse.itk.org/u/crossmanith)\
**Replies:** 2\
**Last updated:** [July 31, 2018, 7:05pm UTC](https://discourse.itk.org/t/lineiterator/1170 "2018-07-31T19:05:01Z")

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I’d like to draw cross hairs in an image. Currently I’m using 4 LineIterators. Is there a way to reuse one iterator and specify new start and end indices for each of the four lines?

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## [Problem about the Itk.js readImageDICOMFileSeries function](https://discourse.itk.org/t/problem-about-the-itk-js-readimagedicomfileseries-function/1167)

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**Author:** [@Mason](https://discourse.itk.org/u/Mason)\
**Replies:** 5\
**Last updated:** [July 31, 2018, 4:17am UTC](https://discourse.itk.org/t/problem-about-the-itk-js-readimagedicomfileseries-function/1167 "2018-07-31T04:17:47Z")

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Hello folks. I have been learning itk.js for several days. I have a problem about the readImageDICOMFileSeries function. Here are some codes I wrote to read a DICOM file series as an itk.js Image object. const files = d…

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## [C1083: cannot open include file: 'vnl/vnl\_vector\_ref.h': No such file or directory](https://discourse.itk.org/t/c1083-cannot-open-include-file-vnl-vnl-vector-ref-h-no-such-file-or-directory/1115)

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**Author:** [@aharris](https://discourse.itk.org/u/aharris)\
**Replies:** 2\
**Last updated:** [July 27, 2018, 9:51pm UTC](https://discourse.itk.org/t/c1083-cannot-open-include-file-vnl-vnl-vector-ref-h-no-such-file-or-directory/1115 "2018-07-27T21:51:46Z")

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Hi, I’m attempting to add a class that builds correctly on its own to a project that was originally built not using cmake. I should say it was working for quite a while, but at some point stopped working without a valid…

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## [Convert itkImageD2 to itkImageF2](https://discourse.itk.org/t/convert-itkimaged2-to-itkimagef2/1149)

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**Author:** [@Hakookaine](https://discourse.itk.org/u/Hakookaine)\
**Replies:** 1\
**Last updated:** [July 25, 2018, 1:16pm UTC](https://discourse.itk.org/t/convert-itkimaged2-to-itkimagef2/1149 "2018-07-25T13:16:42Z")

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Hi everyone ! I need to make a Hough Transform with itk, but when i use SetInput, i need a itkImageF2 or IF2 but my image is an itkImageD2, how can i convert to the good format ? Hakoo’

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## [How to label image with a color pixel value in ITK?](https://discourse.itk.org/t/how-to-label-image-with-a-color-pixel-value-in-itk/1147)

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**Author:** [@srbn.ghosh89](https://discourse.itk.org/u/srbn.ghosh89)\
**Replies:** 2\
**Last updated:** [July 24, 2018, 9:56pm UTC](https://discourse.itk.org/t/how-to-label-image-with-a-color-pixel-value-in-itk/1147 "2018-07-24T21:56:32Z")

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I can see that I can label image from 0 to 255. But I want to label with different colors like red, green. Is there any way to do that?

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## [Problem with image in coronal view](https://discourse.itk.org/t/problem-with-image-in-coronal-view/1144)

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**Author:** [@sz20b5](https://discourse.itk.org/u/sz20b5)\
**Replies:** 1\
**Last updated:** [July 24, 2018, 1:29pm UTC](https://discourse.itk.org/t/problem-with-image-in-coronal-view/1144 "2018-07-24T13:29:17Z")

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Hi, I have an image which is 2d in coronal view(x,z), however if I load the image with ITK, then it reads as it is a typical axial image(x,y). How can I read it as real coronal(x,z) image? Thanks, Sz.U.

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## [ITK Euler3DTransform in MATLAB](https://discourse.itk.org/t/itk-euler3dtransform-in-matlab/1131)

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**Author:** [@alven](https://discourse.itk.org/u/alven)\
**Replies:** 1\
**Last updated:** [July 21, 2018, 9:50pm UTC](https://discourse.itk.org/t/itk-euler3dtransform-in-matlab/1131 "2018-07-21T21:50:01Z")

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Hi! I’m trying to warp a 3D MR image (stored as a nifti-file) to a 3D PET image (stored as a nifti-file) in MATLAB using an Euler3DTransfom transformation matrix from ITK registration. However, the results does not rese…

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## [Access and transfert transformation matrice with simpleITk and 3Dslicer](https://discourse.itk.org/t/access-and-transfert-transformation-matrice-with-simpleitk-and-3dslicer/1128)

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**Author:** [@drcjaudet](https://discourse.itk.org/u/drcjaudet)\
**Replies:** 2\
**Last updated:** [July 18, 2018, 9:09pm UTC](https://discourse.itk.org/t/access-and-transfert-transformation-matrice-with-simpleitk-and-3dslicer/1128 "2018-07-18T21:09:53Z")

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Hello, i work with simpleITK with python in 3dSlicer. We create a transform matrix with general brain registration (Bspline). I would like to pull this matrix into the python Interactor to be able ti play with it. I tr…

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## [\[SOLVED\] Copying Headers after performing operation](https://discourse.itk.org/t/solved-copying-headers-after-performing-operation/1111)

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**Author:** [@thatguy14](https://discourse.itk.org/u/thatguy14)\
**Replies:** 5\
**Last updated:** [July 12, 2018, 3:31pm UTC](https://discourse.itk.org/t/solved-copying-headers-after-performing-operation/1111 "2018-07-12T15:31:06Z")

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Hello! I am fairly new to using ITK. I am trying to use the markov random field filter for segmentation using this as an example. I presegmented the image using the kmeans example. The problem I am having is that the he…

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## [Overlay Several Labels On Top Of An Image](https://discourse.itk.org/t/overlay-several-labels-on-top-of-an-image/1096)

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**Author:** [@Dre](https://discourse.itk.org/u/Dre)\
**Replies:** 7\
**Last updated:** [July 6, 2018, 3:01pm UTC](https://discourse.itk.org/t/overlay-several-labels-on-top-of-an-image/1096 "2018-07-06T15:01:24Z")

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Hello, I am trying to apply several .nrrd labels (binary segmentation masks) on top of an .nrrd image (a CT scan). Am I able to achieve this task thanks to this example : https://itk.org/ITKExamples/src/Filtering/Image…

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## [ITK FFT Module: 1D FFT filters removed/renamed?](https://discourse.itk.org/t/itk-fft-module-1d-fft-filters-removed-renamed/1091)

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**Author:** [@gavinb](https://discourse.itk.org/u/gavinb)\
**Replies:** 2\
**Last updated:** [July 5, 2018, 3:13pm UTC](https://discourse.itk.org/t/itk-fft-module-1d-fft-filters-removed-renamed/1091 "2018-07-05T15:13:02Z")

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Hello, we’d like to use the itk::FFTW1DRealToComplexConjugateImageFilter\< TPixel, Dimension \> class which is documented in: https://itk.org/Doxygen410/html/group\_\_FFT1D.html but the group of 1D filters are no longer pr…

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## [Multithread filter how to write to the same buffer](https://discourse.itk.org/t/multithread-filter-how-to-write-to-the-same-buffer/1029)

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**Author:** [@rolof](https://discourse.itk.org/u/rolof)\
**Replies:** 4\
**Last updated:** [June 25, 2018, 5:30pm UTC](https://discourse.itk.org/t/multithread-filter-how-to-write-to-the-same-buffer/1029 "2018-06-25T17:30:37Z")

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Hi all, I know how to multi-thread works a bit, and I know that the regions of images are passed to different CPU’s core. This process is useful to fill an output image and very convenient. However, I need now to proces…

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## [SimpleITK: Channel storage order?](https://discourse.itk.org/t/simpleitk-channel-storage-order/1027)

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**Author:** [@szhorvat](https://discourse.itk.org/u/szhorvat)\
**Replies:** 1\
**Last updated:** [June 22, 2018, 5:56pm UTC](https://discourse.itk.org/t/simpleitk-channel-storage-order/1027 "2018-06-22T17:56:02Z")

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I am looking at the BufferImportExport example in SimpleITK: https://itk.org/SimpleITKDoxygen/html/BufferImportExport\_8cxx-example.html I was wondering what channel storage order SimpleITK uses. Is it interleaved (i.e.…

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## [SimpleITK: compiling first C++ program](https://discourse.itk.org/t/simpleitk-compiling-first-c-program/1026)

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**Author:** [@szhorvat](https://discourse.itk.org/u/szhorvat)\
**Replies:** 2\
**Last updated:** [June 22, 2018, 2:49pm UTC](https://discourse.itk.org/t/simpleitk-compiling-first-c-program/1026 "2018-06-22T14:49:59Z")

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I managed to compile SimpleITK according to the instructions, and now I would like to start using it from C++. I am looking for guidance on compiling one of the basic examples such as HelloWorld.cxx or SimpleGaussianFun…

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## [ImageToVTKImageFilter usage in python](https://discourse.itk.org/t/imagetovtkimagefilter-usage-in-python/1023)

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**Author:** [@Edern\_Haumont](https://discourse.itk.org/u/Edern_Haumont)\
**Replies:** 0\
**Last updated:** [June 21, 2018, 9:47am UTC](https://discourse.itk.org/t/imagetovtkimagefilter-usage-in-python/1023 "2018-06-21T09:47:55Z")

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Good morning, I am back with another (potentially trivial for a non-beginner) problem ! I have an image read by a ImageSeriesReader. Now I want to pass it through an ImageToVTKImageFilter to get an ImageData and apply…

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## [DICOM reader](https://discourse.itk.org/t/dicom-reader/1018)

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**Author:** [@Edern\_Haumont](https://discourse.itk.org/u/Edern_Haumont)\
**Replies:** 3\
**Last updated:** [June 21, 2018, 9:31am UTC](https://discourse.itk.org/t/dicom-reader/1018 "2018-06-21T09:31:47Z")

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Good morning everyone, I am trying to use the itk GDCM reader in Python. This is what I wrote so far to read from a folder, as a ITK beginner: reader = itk.ImageSeriesReader.New() dicomIO = itk.GDCMImageIO.New() reader…

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## [itkImageToVtkImageFilter returns ObjectBase](https://discourse.itk.org/t/itkimagetovtkimagefilter-returns-objectbase/1019)

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**Author:** [@arwtyxouymz](https://discourse.itk.org/u/arwtyxouymz)\
**Replies:** 9\
**Last updated:** [June 20, 2018, 6:44am UTC](https://discourse.itk.org/t/itkimagetovtkimagefilter-returns-objectbase/1019 "2018-06-20T06:44:36Z")

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Hi, I’m using ITK5 and VTK9, and I’m very confusing about itkImageToVtkImageFilter returns. This is my code class Window { public: Window(); explicit Window(const ImageType::Pointer image); virtual ~Window…

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## [updated tutorial on writing json files for filters code autogeneration](https://discourse.itk.org/t/updated-tutorial-on-writing-json-files-for-filters-code-autogeneration/1001)

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**Author:** [@mkvasnyt](https://discourse.itk.org/u/mkvasnyt)\
**Replies:** 3\
**Last updated:** [June 15, 2018, 1:36pm UTC](https://discourse.itk.org/t/updated-tutorial-on-writing-json-files-for-filters-code-autogeneration/1001 "2018-06-15T13:36:39Z")

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Dear all, I am attempting to create a json file for my own mock ITK-filter and having troubles when compiling SimpleITK. I am following this tutorial https://itk.org/SimpleITKDoxygen/html/FilterTemplatesPage.html I hav…

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## [import SimpleITK fails](https://discourse.itk.org/t/import-simpleitk-fails/1009)

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**Author:** [@mkvasnyt](https://discourse.itk.org/u/mkvasnyt)\
**Replies:** 3\
**Last updated:** [June 15, 2018, 1:29pm UTC](https://discourse.itk.org/t/import-simpleitk-fails/1009 "2018-06-15T13:29:31Z")

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Dear all, I’ve built and tested custom version of SimpleITK on MacOS Sierra 10.12.5. 99% of tests passed, from Python tests only 2 failed. I also see that newly built SimpleITK package is successfully installed to roo…

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## [Getting Dicom file paths of study from DCMTK archive](https://discourse.itk.org/t/getting-dicom-file-paths-of-study-from-dcmtk-archive/1007)

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**Author:** [@benjaminhon](https://discourse.itk.org/u/benjaminhon)\
**Replies:** 0\
**Last updated:** [June 15, 2018, 9:59am UTC](https://discourse.itk.org/t/getting-dicom-file-paths-of-study-from-dcmtk-archive/1007 "2018-06-15T09:59:55Z")

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Hi all, Currently, i am trying to download files from a PACS and then open them from ITK. I am starting a DCMQRSCP server, and using MOVESCU to download images into my local DCMQRSCP archive. However, DCMTK stores the …

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## [Get zero size when read an image](https://discourse.itk.org/t/get-zero-size-when-read-an-image/1005)

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**Author:** [@Lianli\_Liu](https://discourse.itk.org/u/Lianli_Liu)\
**Replies:** 1\
**Last updated:** [June 15, 2018, 9:05am UTC](https://discourse.itk.org/t/get-zero-size-when-read-an-image/1005 "2018-06-15T09:05:28Z")

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I tried to use the following code to read an image #include “itkImageFileReader.h” #include “itkImage.h” int main(int argc, char \* argv\[\]){ const unsigned int Dimension = 3; typedef float PixelType; …

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## [Compile landmark based registration](https://discourse.itk.org/t/compile-landmark-based-registration/995)

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**Author:** [@Lianli\_Liu](https://discourse.itk.org/u/Lianli_Liu)\
**Replies:** 1\
**Last updated:** [June 13, 2018, 11:21am UTC](https://discourse.itk.org/t/compile-landmark-based-registration/995 "2018-06-13T11:21:52Z")

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I am trying to compile this WiKi example https://itk.org/Wiki/ITK/Examples/Registration/LandmarkBasedTransformInitializer, but got several errors such as error: variable or field ‘CreateFixedImage’ declared void void …

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## [Bspline control points clarification](https://discourse.itk.org/t/bspline-control-points-clarification/981)

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**Author:** [@adlerjohn557](https://discourse.itk.org/u/adlerjohn557)\
**Replies:** 4\
**Last updated:** [June 13, 2018, 7:31pm UTC](https://discourse.itk.org/t/bspline-control-points-clarification/981 "2018-06-13T19:31:23Z")

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Hi, I’m trying to understand the underlying logic regarding control points in BSplineTransformInitializer. Specifically, the information regarding the control points’ location in the space. I have searched here and foun…

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## [scale parameters optimizer registration](https://discourse.itk.org/t/scale-parameters-optimizer-registration/990)

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**Author:** [@pdeman](https://discourse.itk.org/u/pdeman)\
**Replies:** 0\
**Last updated:** [June 11, 2018, 10:17am UTC](https://discourse.itk.org/t/scale-parameters-optimizer-registration/990 "2018-06-11T10:17:05Z")

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Hi, I have a code working with Normalized Correlation for the coregistration. The optimizer is set like that (from an example I found): Superclass::m\_Optimizer-\>MinimizeOn(); Superclass::m\_Optimizer-\>SetMaximumStepLe…

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## [\[SOLVED\] Build RTK as external module for another module](https://discourse.itk.org/t/solved-build-rtk-as-external-module-for-another-module/986)

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**Author:** [@Gordian](https://discourse.itk.org/u/Gordian)\
**Replies:** 13\
**Last updated:** [June 9, 2018, 9:27pm UTC](https://discourse.itk.org/t/solved-build-rtk-as-external-module-for-another-module/986 "2018-06-09T21:27:26Z")

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Hi, After figuring out how to create a new module I wanted to create some tests for the module using the testdriver provided by the module template. I added an external module (RTK) and this works fine. An error occur…

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## [itk python blocking pyqt gui](https://discourse.itk.org/t/itk-python-blocking-pyqt-gui/983)

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**Author:** [@benjaminhon](https://discourse.itk.org/u/benjaminhon)\
**Replies:** 2\
**Last updated:** [June 11, 2018, 8:44am UTC](https://discourse.itk.org/t/itk-python-blocking-pyqt-gui/983 "2018-06-11T08:44:43Z")

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Hi, I’ve been trying to run itk functions in a separate thread pool, so far printing the current thread from the function shows that it is not being run on the main thread. However, running itk functions on a separate t…

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## [Get values of image within sphere spatial object](https://discourse.itk.org/t/get-values-of-image-within-sphere-spatial-object/989)

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**Author:** [@G\_Tom](https://discourse.itk.org/u/G_Tom)\
**Replies:** 0\
**Last updated:** [June 9, 2018, 1:13pm UTC](https://discourse.itk.org/t/get-values-of-image-within-sphere-spatial-object/989 "2018-06-09T13:13:42Z")

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Hi all, Here is what I need, I have and image , could be 2d or 3d, I want to extract all values of image lying in a spherical region defined by a spatial object sphere of given radius. Thanks

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## [Issues with bounded deformable registration \[SOLVED\]](https://discourse.itk.org/t/issues-with-bounded-deformable-registration-solved/964)

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**Author:** [@BradG89](https://discourse.itk.org/u/BradG89)\
**Replies:** 1\
**Last updated:** [June 7, 2018, 3:13pm UTC](https://discourse.itk.org/t/issues-with-bounded-deformable-registration-solved/964 "2018-06-07T15:13:26Z")

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Hello, I’ve been utilizing a module in an image processing program 3D Slicer and it has the ability to perform BSpline Registration when the registration is unbounded or when the image’s physical coordinates can move wi…

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