How does exactly ITK-SNAP store ROI labels?

[JM]

I'm not sure whether the name of the ROI labels are stored in the nifti file or in ITK-SNAP thus storing which labels belong to the scans I open.

I tried to find those label names in the nifti files opening them in python with the nibabel library but I couldn't find them, so I was wondering whether there is no information about it stored in the files and it's therefore ITK-SNAP who stores it somewhere.

[Dzenan Zukic]

It looks like it is stored per-file in user folder. On Windows, it is %AppData%\itksnap.org\ITK-SNAP\ImageAssociations which expands to C:\Users\Dzenan\AppData\Roaming\itksnap.org\ITK-SNAP\ImageAssociations on my computer.

Regards,

Dženan

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[Paul Yushkevich]

Labels cannot be stored in NIFTI files. They are stored in "image association" files created in the directory that Dzenan noted. For each NII file that you open an association file is created. That way when you open the same file again, the labels are remembered.

You can export labels as a text file from the Segmentation menu

Best

Paul

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania