Index

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:

  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.

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

make_average_subject (last edited 2017-12-19 10:19:48 by MorganFogarty)