Name

make_average_surface

Description

Creates average surfaces and curvatures from a set of subjects. Calls mris_average_curvature, mris_make_average_surface, mris_smooth, mris_inflate, and mris_curvature.

Synopsis

make_average_surface [options] --subjects <subjects> --fsgd fsgdfile

Arguments

Required Flagged Arguments

--subjects <subj1> <subj2> ...	Also can declare subjects in SUBJECTS env variable
--fsgd fsgdfile	Get subject list from fsgd

Optional Flagged Arguments

--out <average subject name>	Default name is 'average'
--sdir <SUBJECTS_DIR to use instead of the one in the env>
--sd	Same as -sdir
--sd-out topdir	Put data here
--xform <transform_fname>	Filename of transform file
--ico <number>	Specify icosahedron number, default is 7 (ic7.tri)
--surf-reg <surface name>	Alternative registration surface
--lh	Only do left hemi (default is to do both)
--rh	Only do right hemi (default is to do both)
--force	Overwrite existing average subject data
--no-annot	Do not use annotation when making template tif
--template-only	Useful when creating iterative atlases
--no-symlink	Do not use symbolic links (just copy files)
--no-lik	Same as --no-symlink
--help	Short descriptive help
--version	Script version info
--echo	Enable command echo, for debugging
--debug	Same as --echo

Examples

Example 1

make_average_surface --out avgsubject --subjects subj1 subj2 subj3 subj4

Will create $SUBJECTS_DIR/avgsubject with average surfaces for orig, white, pial, inflated for each hemi.

Reporting Bugs

Report bugs to freesurfer@nmr.mgh.harvard.edu