ITK-Snap

As ITK-snap is heavily graphics and interactive, it is generally recommended to run the program from a VGL node. However, it does reasonably well on other nodes. So if you feel you need the additional memory – running from e.g. a bigmem-node is fine ..

# – How to launch (on VGLnode / Graphics node) – #

• Launch a terminal on the Graphics node type
• Call the following commands in the terminal:
• cd /dtu/3d-imaging-center/
• . shortcuts/itk-snap.sh

# – How to launch (on other nodes) – #

• Launch a terminal on desired node type
• Call the following commands in the terminal:
• cd /dtu/3d-imaging-center/QIM/itk-snap/bin
• itk-snap

# – File type support – #
As ITK-snap is originally made for neuroimaging, the supported formats are mostly the standard medical ones:

• Nifty (.nii)
• DICOM (.dcm)
• ..

Note: It can also load .tiff stacks – called generic ITK in the program. However, metadata such as voxel spacing and coordinate system information is not available in this format.

Tips and tricks for using ITK-snap

Guide: Advanced_image_analysis_note