Index

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.

See Also

make_average_subject, make_average_volume

Reporting Bugs

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

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