A CLI tool to extract ROIs from Freesurfer segmentation file
A CLI tool to convert Freesurfer segmentations into separate NifTi files
Install this package using
pip install fsmakeroi
The command context for running this tool is:
fsmakeroi [OPTIONS] aseg rois
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
fsmakeroi -i [PATH TO IMAGE] aseg rois
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