USAGE: make_average_subject

Required Arguments

• --subjects <subj1> <subj2> ... <subjN>

  • : or declare subjects in SUBJECTS env var
  --fsgd fsgdfile : get subject list from fsgd

Optional Arguments

• --out <average subject name> : default name is 'average' --sd-out sdout : put output under sdout instead of SUBJECTS_DIR --link : link back to the original SUBJECTS_DIR with --sd-out --sdir <SUBJECTS_DIR to use instead of the one in the env> --sd : same as --sdir --xform <transform_fname> : filename of transform file --no-surf : do not make average surfaces --no-vol : do not make average volumes --force : overwrite existing average subject data --help : short descriptive help --version : script version info --echo : enable command echo, for debug --debug : same as --echo

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:

• (1) on the command-line with --subjects (2) through the SUBJECTS environment variable

  (3) specifying a FreeSurfer Group Descriptor (FSGD) file. The FSGD is

  • used by freesurfer to specify designs for statistical analysis. See surfer.nmr.mgh.harvard.edu/docs/fsgdf.txt.

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:

• make_average_subject --out avgsubject --subjects subj1 subj2 subj3 subj4

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:

• setenv SUBJECTS = (subj1 subj2 subj3 subj4) make_average_subject --out avgsubject

will do the same as Example 1.

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

• tkregister2 --fstal --s avgsubject --mgz

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

• tkmedit avgsubject orig.mgz lh.white

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