osl_ephys.source_recon.freesurfer_utils#

Wrappers for Freesurfer.

Functions#

`setup_freesurfer`(directory[, subjects_dir])	Setup FreeSurfer.
`check_freesurfer`()	Check FreeSurfer is installed.
`get_freesurfer_filenames`(subjects_dir, subject)	Get paths to all FreeSurfer files.
`get_coreg_filenames`(subjects_dir, subject)	Files used in coregistration by FreeSurfer.
`recon_all`(smri_file, subjects_dir, subject)
`make_watershed_bem`(outdir, subject, **kwargs)	Wrapper for `mne.bem.make_watershed_bem` making a watershed BEM with FreeSurfer.
`make_fsaverage_src`(subjects_dir[, spacing])

Module Contents#

osl_ephys.source_recon.freesurfer_utils.setup_freesurfer(directory, subjects_dir=None)[source]#

Setup FreeSurfer.

Parameters:: directory (str) – Path to FreeSurfer installation.

osl_ephys.source_recon.freesurfer_utils.check_freesurfer()[source]#: Check FreeSurfer is installed.

osl_ephys.source_recon.freesurfer_utils.get_freesurfer_filenames(subjects_dir, subject)[source]#

Get paths to all FreeSurfer files.

Files will be in subjects_dir/subject/.

Parameters:

subjects_dir (string) – Directory containing the subject directories.
subject (string) – Subject directory name to put the coregistration files in.

Returns:

files – A dict of files generated and used by RHINO. Contains three keys: - ‘surf’: containing surface extraction file paths. - ‘coreg’: containing coregistration file paths. - ‘fwd_model’: containing the forward model file path.

Return type:

dict

osl_ephys.source_recon.freesurfer_utils.get_coreg_filenames(subjects_dir, subject)[source]#

Files used in coregistration by FreeSurfer.

Files will be in subjects_dir/subject/.

Parameters:

subjects_dir (string) – Directory containing the subject directories.
subject (string) – Subject directory name to put the coregistration files in.

Returns:

filenames – A dict of files generated and used by FreeSurfer.

Return type:

dict

osl_ephys.source_recon.freesurfer_utils.recon_all(smri_file, subjects_dir, subject)[source]#

osl_ephys.source_recon.freesurfer_utils.make_watershed_bem(outdir, subject, **kwargs)[source]#: Wrapper for mne.bem.make_watershed_bem making a watershed BEM with FreeSurfer.

osl_ephys.source_recon.freesurfer_utils.make_fsaverage_src(subjects_dir, spacing='oct6')[source]#