freesurfer - Methods to run Freesurfer analyses

class neural.freesurfer.FreesurferDir(subj_dir, subj_id)

Class to interact with a freesurfer-organized directory

dir_name = None

The individual subject’s directory (i.e., “[subj_dir]/[subj_id]”)

skull_strip = None

Path to the skull-stripped anatomy

subj_dir = None

The parent subjects directory (the SUBJECTS_DIR environment variable)

subj_id = None

The individual subject id

neural.freesurfer.guess_home()

If freesurfer_home is not set, try to make an intelligent guess at it

neural.freesurfer.mgz_to_nifti(filename, prefix=None, gzip=True)

Convert filename to a NIFTI file using mri_convert

neural.freesurfer.parpar_dir(d)

parent of parent directory of file: e.g., this_dir/other_dir/filename

neural.freesurfer.recon_all(subj_id, anatomies)

Run the recon_all script

neural.freesurfer.setup_freesurfer()

Setup the freesurfer environment variables