A CLI tool to extract ROIs from Freesurfer segmentation file
Project description
FSMakeROI
A CLI tool to convert Freesurfer segmentations into separate NifTi files
Installation
Install this package using pip with:
pip install fsmakeroi
Usage
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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