FreeSurfer and BIDS

To properly structure a freesurfer derivative, SUBJECTS_DIR should point to the appropriate <pipeline> directory. Cross-sectional subjects or subject-specific templates should be named with the following syntax:

freesurfer/
    sub-<subject_label>/
        /mri
        /surf
        ...

Longitudinal

Similarly, individual sessions from longitudinal studies should be organized as:

freesurfer/
    sub-<subject_label>_ses-<session_label>/

Longitudinal templates should use the sub-<subject_label> subject name. This will produce longitudinally-processed sessions in the unbiased template space with the following names:

freesurfer/
    sub-<subject_label>_ses-<session_label>.long.sub-<subject_label>/

not yet implemented...

By default, freesurfer-processed subjects are not BIDS compatible, but supplying the --bids-out flag to recon-all will convert commonly-used output to BIDS-formatted files in a new anat subdirectory. This will also create a top-level labels.tsv structure-lookup-table in $SUBJECTS_DIR (converted from $FREESURFER_HOME/FreeSurferColorLUT.txt). The most up-to-date version of labels.tsv can be downloaded here.