USAGE: make_average_subject

Required Arguments

Optional Arguments

Version: $Id: make_average_subject,v 1.7.2.1 2006/06/09 15:46:28 nicks Exp $

Creates average subject by averaging surfaces, curvatures, and volumes from a set of subjects. The surface is a 7th order icosahedron tesselation. For surfaces, the XYZ coordinate of a vertex is computed as the average talairach coordinate of that vertex in each subject. The talairach coordinate is based on talairach.xfm (unless changed with --xform), so the individual talairachs must be accurate for the final coordinate to be meaningful. Note that even though talairach coordinates are used for surfaces, all surface-based averaging is done using the surface atlas (NOT talairach averaging!).

Calls make_average_surface and make_average_volume. See these programs for specific help.

The subject list can be specified in one of three ways:

The output will be created in SUBJECTS_DIR/averagesubjectname unless --topdir is specified. In this case, the data are stored in topdir/averagesubjectname, and a link is created to SUBJECTS_DIR/averagesubjectname. This can convenient when your the disk that hosts your SUBJECTS_DIR starts to get full.

EXAMPLES

Example 1:

will create $SUBJECTS_DIR/avgsubject with average surfaces for orig, white, pial, inflated for each hemi. It will also create average volumes for orig, brain, and T1. Notice that the '--out avgsubject' is merely overriding the default output name 'average'.

Example 2:

will do the same as Example 1.

Example 3: check that the average subject volume aligns with the talairach subject:

Example 4: check that the average subject surfaces align with the volume:

You should see that the surfaces more-or-less align with the folds. Remember this is talairach, so the volume will be blurry.

SEE ALSO

make_average_volume, make_average_surface, recon-all, make_final_surfaces, morph_subject