osl_ephys.source_recon.freesurfer_utils ======================================= .. py:module:: osl_ephys.source_recon.freesurfer_utils .. autoapi-nested-parse:: Wrappers for Freesurfer. Functions --------- .. autoapisummary:: osl_ephys.source_recon.freesurfer_utils.setup_freesurfer osl_ephys.source_recon.freesurfer_utils.check_freesurfer osl_ephys.source_recon.freesurfer_utils.get_freesurfer_filenames osl_ephys.source_recon.freesurfer_utils.get_coreg_filenames osl_ephys.source_recon.freesurfer_utils.recon_all osl_ephys.source_recon.freesurfer_utils.make_watershed_bem osl_ephys.source_recon.freesurfer_utils.make_fsaverage_src Module Contents --------------- .. py:function:: setup_freesurfer(directory, subjects_dir=None) Setup FreeSurfer. :param directory: Path to FreeSurfer installation. :type directory: str .. py:function:: check_freesurfer() Check FreeSurfer is installed. .. py:function:: get_freesurfer_filenames(subjects_dir, subject) Get paths to all FreeSurfer files. Files will be in subjects_dir/subject/. :param subjects_dir: Directory containing the subject directories. :type subjects_dir: string :param subject: Subject directory name to put the coregistration files in. :type subject: string :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. :rtype: dict .. py:function:: get_coreg_filenames(subjects_dir, subject) Files used in coregistration by FreeSurfer. Files will be in subjects_dir/subject/. :param subjects_dir: Directory containing the subject directories. :type subjects_dir: string :param subject: Subject directory name to put the coregistration files in. :type subject: string :returns: **filenames** -- A dict of files generated and used by FreeSurfer. :rtype: dict .. py:function:: recon_all(smri_file, subjects_dir, subject) .. py:function:: make_watershed_bem(outdir, subject, **kwargs) Wrapper for :py:func:`mne.bem.make_watershed_bem ` making a watershed BEM with FreeSurfer. .. py:function:: make_fsaverage_src(subjects_dir, spacing='oct6')