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I am running on Ubuntu. When calling the Show method of SimpleITK I am not being able to view such image in my FIJI ( ImageJ2) window.

Given that FIJI is a portable application, is it necessary to perform some more process in order to properly link Show method with it?

Thanks in advance

Francisco Cunha
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1 Answers1

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SimpleITK requires an external image viewer to display images (ImageJ, 3DSlicer, ITK-Snap, etc).

ImageJ Installation

  1. Go to https://imagej.nih.gov/ij/download.html
  2. Make sure to download the bundled with 64-bit Java 1.8.0_112 version

ImageJ Setup

  1. Go to https://imagej.nih.gov/ij/plugins/nifti.html
  2. Download nifti_io.jar
  3. Go to C:\blah\blah\ImageJ\plugins\Input-Output
  4. Delete the existing nifti_io.jar file from the folder
  5. Copy the downloaded nifti_io.jar file into the folder
  6. Restart ImageJ and check if File -> Import -> NIfTI-Analyze is there
  7. If it is there, the plugin was successfully installed

SimpleITK Setup

  1. Find the path where your ImageJ.exe file exists
  2. Open cmd
  3. Type in setx SITK_SHOW_COMMAND "C:\blah\blah\ImageJ\ImageJ.exe"
  4. You should get the message SUCCESS: Specified value was saved

Check if everything works

  1. Restart your text editor or IDE (if it was already open)
  2. Run your code
Senyokbalgul
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