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| 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]]. | 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]]. |
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.