'''Index'''
<<TableOfContents>>

= 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