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.


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


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>


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


Only do left hemi (default is to do both)


Only do right hemi (default is to do both)


Overwrite existing average subject data


Do not use annotation when making template tif


Useful when creating iterative atlases


Do not use symbolic links (just copy files)


Same as --no-symlink


Short descriptive help


Script version info


Enable command echo, for debugging


Same as --echo


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.

See Also

make_average_subject, make_average_volume

Reporting Bugs

Report bugs to

make_average_surface (last edited 2017-12-19 10:52:09 by MorganFogarty)