= 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 [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/labels.tsv|here]].