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A CLI tool to extract ROIs from Freesurfer segmentation file

Project description


A CLI tool to convert Freesurfer segmentations into separate NifTi files


Install this package using pip with:

pip install fsmakeroi


The command context for running this tool is:

fsmakeroi [OPTIONS] aseg rois

Where aseg is the path to aparc+aseg.mgz file, and rois is the the path to text file containing Freesurfer ROI LUT codes.

The ROI code file is a list of ROIs to extract, with each line being the code to corresponding ROI. Please refer to /examples/example_rois.txt for an example on creating the code file.

ROIs can also be applied to any images as long as they are registered to T1 in Freesurfer space. This is done with the -i or --image flag:

fsmakeroi -i [PATH TO IMAGE] aseg rois

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