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.

Reporting Bugs

Report bugs to freesurfer@nmr.mgh.harvard.edu

-Deletions are marked like this.
+Additions are marked like this.
 Line 8:
+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.
-Line 10:
+Line 35:
+make_average_subject --subjects <subjects> --fsgd fsgdfile [options]
-Line 14:
+Line 40:
+|| --subjects <subj1> <subj2> ... || Also can declare subjects in SUBJECTS env variable ||

|| --fsgd fsgdfile || Get subject list from fsgd ||
-Line 16:
+Line 44:
+|| --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 ||
-Line 50:
+Line 91:
-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.