surf_laynii

Script that enables LAYNII layering using Freesurfer segmentations You may need to run chmod +x surf_laynii to make it an executable.

Example use

surf_laynii -d /home/user/Data/Project-01/fs_recons -s sub-01

Optional use cases

In case you want the rim files but want to run LAYNII with different parameters, or want to register the rim file to EPI space & only then running LAYNII, use the stop laynii flag '-l'.
surf_laynii -d /home/user/Data/Project-01/fs_recons -s sub-01 -l

In case you want the rim files at a resolution higher/lower than the 0.3 mm default.
surf_laynii -d /home/user/Data/Project-01/fs_recons -s sub-01 -n 0.2