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