Index
Contents
Name
make_average_subject
Description
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:
- on the command-line with --subjects
- through the SUBJECTS environment variable
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.
Synopsis
make_average_subject --subjects <subjects> --fsgd fsgdfile [options]
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' |
--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 debugging |
--debug |
Same as --echo |
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
tkregister2 --fstal --s avgsubject --mgz
Checks that the average subject volume aligns with the talairach subject:
Example 4
tkmedit avgsubject orig.mgz lh.white
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
Reporting Bugs
Report bugs to freesurfer@nmr.mgh.harvard.edu