# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=32

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**Page:** 33

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## [How to merge two labels in an labeled image](https://discourse.itk.org/t/how-to-merge-two-labels-in-an-labeled-image/2595)

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**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 2\
**Last updated:** [January 9, 2020, 2:12pm UTC](https://discourse.itk.org/t/how-to-merge-two-labels-in-an-labeled-image/2595 "2020-01-09T14:12:28Z")

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I have an image with three or four labels and i want to merge two of them and label it as a single label. How to do it? Convert 3D GUI is not helping me regarding this. Any way through ITK Snap or slicer or ITK modules a…

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## [TileImageFilter and Direction/Orientation](https://discourse.itk.org/t/tileimagefilter-and-direction-orientation/2592)

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**Author:** [@spinicist](https://discourse.itk.org/u/spinicist)\
**Replies:** 2\
**Last updated:** [January 8, 2020, 1:29pm UTC](https://discourse.itk.org/t/tileimagefilter-and-direction-orientation/2592 "2020-01-08T13:29:34Z")

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Hello, (Apologies, I feel like I asked this question a long time ago and maybe I forgot the answer). I am combing several 3D volumes into a 4D series with TileImageFilter. TileImageFilter does not take account of the d…

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## [When we will see the ITK 5 stable release in Debian?](https://discourse.itk.org/t/when-we-will-see-the-itk-5-stable-release-in-debian/2580)

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**Author:** [@ZSmain](https://discourse.itk.org/u/ZSmain)\
**Replies:** 2\
**Last updated:** [January 3, 2020, 7:12pm UTC](https://discourse.itk.org/t/when-we-will-see-the-itk-5-stable-release-in-debian/2580 "2020-01-03T19:12:48Z")

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It’s known that Debian, the stable release will only ship stable releases of packages, but Its not there yet, not even in the testing release! Is there an official responsible for packaging ITK binaries and development …

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## [The program seems suspended (or halted) when it reached to the line Updating the Simplex filter](https://discourse.itk.org/t/the-program-seems-suspended-or-halted-when-it-reached-to-the-line-updating-the-simplex-filter/2555)

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**Author:** [@Sara\_Caffe](https://discourse.itk.org/u/Sara_Caffe)\
**Replies:** 5\
**Last updated:** [December 22, 2019, 4:00pm UTC](https://discourse.itk.org/t/the-program-seems-suspended-or-halted-when-it-reached-to-the-line-updating-the-simplex-filter/2555 "2019-12-22T16:00:50Z")

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Hi everyone, I followed all the comments here, and I am trying to apply the deformation as a post-processing step for the segmentation results. I have applied this algorithm to my data. I have the following files: a m…

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## [vtkTypeMacro compile error](https://discourse.itk.org/t/vtktypemacro-compile-error/2559)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 1\
**Last updated:** [December 21, 2019, 7:47am UTC](https://discourse.itk.org/t/vtktypemacro-compile-error/2559 "2019-12-21T07:47:53Z")

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Hi, any body know what is the header for vtkTypeMacro, I definition of it in vtkSetGet.h, but even that could not remove the compile error?! any ideas how to fix this? Regards, sag

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## [vtk polydata file](https://discourse.itk.org/t/vtk-polydata-file/2558)

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**Author:** [@nour](https://discourse.itk.org/u/nour)\
**Replies:** 3\
**Last updated:** [December 20, 2019, 9:28pm UTC](https://discourse.itk.org/t/vtk-polydata-file/2558 "2019-12-20T21:28:35Z")

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I used to convert nifti file to .vtk file but what I noticed that there are many versions. I need # vtk DataFile Version 3.0 but this code gives me # vtk DataFile Version 4.2. import vtk import sys reader = vtk.vtkNIF…

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## [how to modify Medical4 example of vtk to accept DICOM format slices](https://discourse.itk.org/t/how-to-modify-medical4-example-of-vtk-to-accept-dicom-format-slices/2549)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 4\
**Last updated:** [December 20, 2019, 12:48pm UTC](https://discourse.itk.org/t/how-to-modify-medical4-example-of-vtk-to-accept-dicom-format-slices/2549 "2019-12-20T12:48:37Z")

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Hi, I am trying to replace quarter.1…quater.xx with quarter1.dcm…quarterxx.dcm, questions: what is the format of headsq/quarter.1…quarter.xx? how to convert DICOM slices to headsq slice formats? would be that fixed w…

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## [DICOMSeriesImageReadWrite2.cxx view nrrd file online or MFC or frontend javascript or html5](https://discourse.itk.org/t/dicomseriesimagereadwrite2-cxx-view-nrrd-file-online-or-mfc-or-frontend-javascript-or-html5/2541)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 4\
**Last updated:** [December 18, 2019, 7:57pm UTC](https://discourse.itk.org/t/dicomseriesimagereadwrite2-cxx-view-nrrd-file-online-or-mfc-or-frontend-javascript-or-html5/2541 "2019-12-18T19:57:06Z")

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Hi, I used the DicomSeriesImageReadWrite2.cxx to read a Dicom series of 207 dicom files. It seems working now but I created a huge nrrd file which takes forever to view with UCLA online Brian viewer, any idea if there i…

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## [GussianExample.java in SimpleITK example](https://discourse.itk.org/t/gussianexample-java-in-simpleitk-example/2524)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 14\
**Last updated:** [December 18, 2019, 3:30pm UTC](https://discourse.itk.org/t/gussianexample-java-in-simpleitk-example/2524 "2019-12-18T15:30:59Z")

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Hi, I installed my simpleitk for Java and gladly used the gaussian Example of it in the manual to be exact it is called GaussianExample.java. problem is that I don’t know what kind of image format to use as input and ou…

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## [Importing image from array and axis reorder](https://discourse.itk.org/t/importing-image-from-array-and-axis-reorder/1192)

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**Author:** [@fedorov](https://discourse.itk.org/u/fedorov)\
**Replies:** 14\
**Last updated:** [December 16, 2019, 8:01pm UTC](https://discourse.itk.org/t/importing-image-from-array-and-axis-reorder/1192 "2019-12-16T20:01:54Z")

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I am creating image from a numpy array, using itk-python, and I see that it reorders the array axes: print("Array shape: "+str(scanArray.shape)) scanVolume = itk.GetImageFromArray(scanArray) print("Image shape: "+str(sc…

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## [itk-vtkglue for Python 3.7](https://discourse.itk.org/t/itk-vtkglue-for-python-3-7/1679)

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**Author:** [@alkamid](https://discourse.itk.org/u/alkamid)\
**Replies:** 8\
**Last updated:** [December 16, 2019, 3:01pm UTC](https://discourse.itk.org/t/itk-vtkglue-for-python-3-7/1679 "2019-12-16T15:01:41Z")

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I am trying to use itk.VTKImageToImageFilter, but I believe I need itk-vtkglue for that. Unfortunately, a Python 3.7-compatible version is not available on PyPI (https://pypi.org/project/itk-vtkglue/#files). Would it be …

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## [After casting the ImageType to a new data type, ConnectedComponentImageFilter still raising " error: conversion from ‘itk::Concept::IsInteger\<float\>"](https://discourse.itk.org/t/after-casting-the-imagetype-to-a-new-data-type-connectedcomponentimagefilter-still-raising-error-conversion-from-itk-isinteger-float/2462)

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**Author:** [@Sara\_Caffe](https://discourse.itk.org/u/Sara_Caffe)\
**Replies:** 2\
**Last updated:** [December 15, 2019, 4:55pm UTC](https://discourse.itk.org/t/after-casting-the-imagetype-to-a-new-data-type-connectedcomponentimagefilter-still-raising-error-conversion-from-itk-isinteger-float/2462 "2019-12-15T16:55:55Z")

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I have defined the input ImageType as float and the OutputImageType for the ConnectedComponentImageFilter according to the link: typedef float PixelType; constexpr unsigned int Dimension=3; using ImageType=itk::Image\<Pi…

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## [SimpleITK, ResampleImageFilter for orthogonal views of MRI data](https://discourse.itk.org/t/simpleitk-resampleimagefilter-for-orthogonal-views-of-mri-data/1878)

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**Author:** [@TanjaIvanovska](https://discourse.itk.org/u/TanjaIvanovska)\
**Replies:** 5\
**Last updated:** [December 13, 2019, 2:24pm UTC](https://discourse.itk.org/t/simpleitk-resampleimagefilter-for-orthogonal-views-of-mri-data/1878 "2019-12-13T14:24:16Z")

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Dear All, i have the following question: i have an MRI dataset and would like to compute the other two orthogonal projections of that dataset. If i understand correctly, ResampleImageFilter should do what i need. But i…

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## [build and install SimpleITK on windows 10 error](https://discourse.itk.org/t/build-and-install-simpleitk-on-windows-10-error/2520)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 3\
**Last updated:** [December 12, 2019, 7:56pm UTC](https://discourse.itk.org/t/build-and-install-simpleitk-on-windows-10-error/2520 "2019-12-12T19:56:36Z")

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Hi, I cloned SimpleITK to my windows 10 pc, created src, bin folders and copied SimpleITK source into src, then naturally tried to configure and generate code for vs2017. I get error in configure step says: could not fi…

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## [Sitk composite image](https://discourse.itk.org/t/sitk-composite-image/2514)

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**Author:** [@kayarre](https://discourse.itk.org/u/kayarre)\
**Replies:** 3\
**Last updated:** [December 12, 2019, 7:05pm UTC](https://discourse.itk.org/t/sitk-composite-image/2514 "2019-12-12T19:05:40Z")

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How can one write a composite image to png with sitk? Currently I cast a composite image with three components to vectorUint8, but when I try to write it to file it gives and itk error. Any suggestions or alternatives?

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## [Build ITK with itk\_vtk\_glue](https://discourse.itk.org/t/build-itk-with-itk-vtk-glue/2521)

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**Author:** [@machadoL](https://discourse.itk.org/u/machadoL)\
**Replies:** 5\
**Last updated:** [December 12, 2019, 6:32pm UTC](https://discourse.itk.org/t/build-itk-with-itk-vtk-glue/2521 "2019-12-12T18:32:57Z")

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Guys a very beginner question. I’ve tried to build ITK pointing it to VTK\_build, but no success so far. I’ve done that before, but do not remember and cannot find it elsewhere… Thanks!

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## [Configure and Generate ITK project](https://discourse.itk.org/t/configure-and-generate-itk-project/2522)

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**Author:** [@machadoL](https://discourse.itk.org/u/machadoL)\
**Replies:** 2\
**Last updated:** [December 12, 2019, 5:25pm UTC](https://discourse.itk.org/t/configure-and-generate-itk-project/2522 "2019-12-12T17:25:14Z")

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Guys, another very beginner question. I need to configure and generate an ITK project pointing to a specific ITK-BUILD location via command line. One of the machines I work is not running cmake-gui correctly. Could you…

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## [\[SOLVED\] itkTranslationTransform.h: No such file or directory](https://discourse.itk.org/t/solved-itktranslationtransform-h-no-such-file-or-directory/2510)

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**Author:** [@04jwei](https://discourse.itk.org/u/04jwei)\
**Replies:** 2\
**Last updated:** [December 12, 2019, 11:50am UTC](https://discourse.itk.org/t/solved-itktranslationtransform-h-no-such-file-or-directory/2510 "2019-12-12T11:50:38Z")

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When using make on /home/james/ITK/Examples/RegistrationITKv4, I get the error itkTranslationTransform.h: No such file or directory. I’m a bit confused why this occurs, because ITKGroup\_Core group is selected by default …

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## [\[SOLVED\] Using make on an example leads to error: itkFEMRegistrationFilter.h: No such file or directory](https://discourse.itk.org/t/solved-using-make-on-an-example-leads-to-error-itkfemregistrationfilter-h-no-such-file-or-directory/2505)

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**Author:** [@04jwei](https://discourse.itk.org/u/04jwei)\
**Replies:** 4\
**Last updated:** [December 11, 2019, 3:53pm UTC](https://discourse.itk.org/t/solved-using-make-on-an-example-leads-to-error-itkfemregistrationfilter-h-no-such-file-or-directory/2505 "2019-12-11T15:53:26Z")

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I copied the source code from https://itk.org/Doxygen/html/Examples\_2RegistrationITKv4\_2DeformableRegistration1\_8cxx-example.html into the home/james/ITK-examples/DeformableRegistration1.cxx together with CMakeLists.txt …

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## [Markov Random Field](https://discourse.itk.org/t/markov-random-field/2507)

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**Author:** [@melrobin](https://discourse.itk.org/u/melrobin)\
**Replies:** 6\
**Last updated:** [December 11, 2019, 1:39pm UTC](https://discourse.itk.org/t/markov-random-field/2507 "2019-12-11T13:39:44Z")

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I am trying to run the code here: https://itk.org/Doxygen/html/Examples\_2Statistics\_2ScalarImageMarkovRandomField1\_8cxx-example.html The executable requires two files: BrainT1Slice.png and BrainT1Slice\_labelled.png Th…

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## [Build Documentation](https://discourse.itk.org/t/build-documentation/2506)

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**Author:** [@melrobin](https://discourse.itk.org/u/melrobin)\
**Replies:** 2\
**Last updated:** [December 11, 2019, 3:15am UTC](https://discourse.itk.org/t/build-documentation/2506 "2019-12-11T03:15:04Z")

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What does turning BUILD\_DOCUMENTATION=ON actually do? I was expecting a build of the software guide or files in the /usr/share directory, but this is not produced. Can anyone explain what the output from this flag is?

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## [Reading HDF5 files](https://discourse.itk.org/t/reading-hdf5-files/2503)

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**Author:** [@rdsouza15](https://discourse.itk.org/u/rdsouza15)\
**Replies:** 3\
**Last updated:** [December 10, 2019, 10:24pm UTC](https://discourse.itk.org/t/reading-hdf5-files/2503 "2019-12-10T22:24:28Z")

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Hello, Using the c++ API, I am trying to read in standard HDF5 files but am unable to (See errors below). I have followed the examples online, but to no avail. Has anyone else had similar problems reading in these file…

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## [ITK in Ubuntu 18.04](https://discourse.itk.org/t/itk-in-ubuntu-18-04/2499)

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**Author:** [@banikr](https://discourse.itk.org/u/banikr)\
**Replies:** 1\
**Last updated:** [December 10, 2019, 1:57pm UTC](https://discourse.itk.org/t/itk-in-ubuntu-18-04/2499 "2019-12-10T13:57:01Z")

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While installing ITK in Ubuntu 18.04 I got the following error message: Does not support python version lower than 3.5 But I ran \>\>python3 --version in my terminal and it says python 3.6 installed! How to solve it?

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## [SetForceOrthogonalDirection not having effect](https://discourse.itk.org/t/setforceorthogonaldirection-not-having-effect/2494)

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**Author:** [@EmileSonneveld](https://discourse.itk.org/u/EmileSonneveld)\
**Replies:** 5\
**Last updated:** [December 10, 2019, 6:15am UTC](https://discourse.itk.org/t/setforceorthogonaldirection-not-having-effect/2494 "2019-12-10T06:15:04Z")

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Hi, I got a .dcm serie of images with gantry tilt. I loaded them with ITK5.1 and ITK4.10, but both of them give a skewed image. Using Dicom2Nifti doesn’t have this problem. Photo as example: This is the code I use: a…

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## [rkttutoriablapplicaiton sample, adding volumes](https://discourse.itk.org/t/rkttutoriablapplicaiton-sample-adding-volumes/2489)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 1\
**Last updated:** [December 9, 2019, 1:27pm UTC](https://discourse.itk.org/t/rkttutoriablapplicaiton-sample-adding-volumes/2489 "2019-12-09T13:27:35Z")

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Hi, I work on the rtktutorialapplication project in RTK/applications folder and I have followed instruction in the xxx.cxx file and built it. now I need two volumes as arguments for rtktutorialapplication.exe vol1 vol2. …

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## [Python pycharm and code completion](https://discourse.itk.org/t/python-pycharm-and-code-completion/1697)

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**Author:** [@asertyuio](https://discourse.itk.org/u/asertyuio)\
**Replies:** 16\
**Last updated:** [December 7, 2019, 1:35pm UTC](https://discourse.itk.org/t/python-pycharm-and-code-completion/1697 "2019-12-07T13:35:42Z")

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I’m using pycharm as a python ide. It appears that except in the console, pycharm don’t propose any completion after typing itk module name. Code is running fine. In the python console, completion is working as expected…

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## [How to work with .mha + .raw files](https://discourse.itk.org/t/how-to-work-with-mha-raw-files/2478)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 3\
**Last updated:** [December 6, 2019, 2:54pm UTC](https://discourse.itk.org/t/how-to-work-with-mha-raw-files/2478 "2019-12-06T14:54:08Z")

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Hi, I am trying to see how to read data sets of lets say a ct scan (e.g. sinogram): following are my concerns: how to get the data set of projections. any public site or university site how to use ITK VTK to reconstru…

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## [itk::ImageIO, itk::ImageFileReader, itk::ImageFileWriter, ITK-\>Examples-\>IO-\>RGBImageReadWrite](https://discourse.itk.org/t/itk-imageio-itk-imagefilereader-itk-imagefilewriter-itk-examples-io-rgbimagereadwrite/2476)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 4\
**Last updated:** [December 5, 2019, 4:09pm UTC](https://discourse.itk.org/t/itk-imageio-itk-imagefilereader-itk-imagefilewriter-itk-examples-io-rgbimagereadwrite/2476 "2019-12-05T16:09:53Z")

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Hi, I built the example RGBImageReadWrite.cxx using CMake config generate with CMakeLists.txt and source file for the example and generate bin and built that in vs2017… so far so good, but when I run this example with f…

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## [cannot build Filtering Examples in vs2017](https://discourse.itk.org/t/cannot-build-filtering-examples-in-vs2017/2473)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 2\
**Last updated:** [December 4, 2019, 11:03pm UTC](https://discourse.itk.org/t/cannot-build-filtering-examples-in-vs2017/2473 "2019-12-04T23:03:53Z")

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Hi, I am new to ITK, however very experienced software engineer. I have download, built, and installed ITK on my windows 10 pc. I also have CMake 3.15.4. I created a CMake project using CMakeLists.txt samples in example…

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## [Rotating an Oblique Image](https://discourse.itk.org/t/rotating-an-oblique-image/2470)

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**Author:** [@kleingeo](https://discourse.itk.org/u/kleingeo)\
**Replies:** 2\
**Last updated:** [December 4, 2019, 4:11pm UTC](https://discourse.itk.org/t/rotating-an-oblique-image/2470 "2019-12-04T16:11:21Z")

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I have been trying to rotate an image that has quaterion coordinates and is in an oblique reference frame, but I am not entirely sure how this is done. When I apply the same rotations (two rotations about the x and y axe…

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