FreeSurfer Cortical Stats to Group Table¶

Library: FreeSurfer | Docker Image: freesurfer/freesurfer

Function¶

Collects cortical parcellation statistics across multiple subjects into a single table for group analysis.

Modality: Multiple FreeSurfer subject directories with completed recon-all.

Typical Use: Creating group spreadsheet of cortical morphometry for statistical analysis.

--subjects (subject list), --hemi (hemisphere), --meas (measure: thickness, area, volume), --tablefile (output table)

Creates one row per subject, one column per region. Output table ready for statistical software.

Name	Type	Required	Label	Flag
`subjects_dir`	`Directory`	Yes	FreeSurfer SUBJECTS_DIR
`fs_license`	`File`	Yes	FreeSurfer license file
`subjects`	`string[]`	Yes	List of subject names	`--subjects`
`hemi`	`enum`	Yes	Hemisphere (lh or rh)	`--hemi`
`tablefile`	`string`	Yes	Output table filename	`--tablefile`
`parc`	`string`	No	Parcellation name (default aparc)	`--parc`
`meas`	`enum`	No	Measurement to extract	`--meas`
`delimiter`	`enum`	No	Delimiter for output table	`--delimiter`
`subjectsfile`	`File`	No	File containing subject list	`--subjectsfile`
`skip`	`boolean`	No	Skip subjects with missing data	`--skip`
`parcid_only`	`boolean`	No	Only output parcellation IDs	`--parcid-only`
`common_parcs`	`boolean`	No	Only output parcels common to all subjects	`--common-parcs`
`report_rois`	`boolean`	No	Report which ROIs differ	`--report-rois`
`transpose`	`boolean`	No	Transpose output table	`--transpose`

Name	Type	Glob Pattern
`table`	`File`	`$(inputs.tablefile)`
`log`	`File`	`aparcstats2table.log`

meas: area, volume, thickness, thicknessstd, meancurv, gauscurv, foldind, curvind

delimiter: tab, comma, space, semicolon

Available versions: latest, 8.1.0, 8.0.0, 7.2.0, 7.3.0, 7.3.1, 7.3.2, 7.4.1, 7.1.1, 6.0