How to use ITK-SNAP for visualization instead of ImageJ in simpleITK python

I have been using ImageJ for visualization. Is there any way to use ITK SNAP or 3D slicer for this purpose?

Hello @unicorn,

Yes, that is easily done. Please go over this jupyter notebook which illustrates the various options for image display.


A similar things can be accomplished by using the ImageViewer as well.

Here’s how I set Slicer to be the viewing app for SimpleITK.Show:

export SITK_SHOW_COMMAND=/Applications/

Basically you set the SITK_SHOW_COMMAND environment variable to point to your viewing application. Show will then invoke the command with the image on the command line.

If you want to see exactly what Show is doing, you can set the debugOn parameter to True.

1 Like