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USAGE: make_average_subject '''Index'''
<<TableOfContents>>
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Required Arguments
   --subjects <subj1> <subj2> ... <subjN>
             : or declare subjects in SUBJECTS env var
   --fsgd fsgdfile : get subject list from fsgd		 = Name =
make_average_subject
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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 $
 = Description =
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EXAMPLES = Synopsis =
make_average_subject --subjects <subjects> --fsgd fsgdfile [options]
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Example 1: = Arguments =
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  make_average_subject --out avgsubject --subjects subj1 subj2 subj3 subj4 == Required Flagged Arguments ==
|| --subjects <subj1> <subj2> ... || Also can declare subjects in SUBJECTS env variable ||
|| --fsgd fsgdfile || Get subject list from fsgd ||
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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'.		 == 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 ||
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Example 2: = 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'.
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== Example 2 ==
{{{
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}}}
Will do the same as Example 1
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will do the same as Example 1. == Example 3 ==
{{{
tkregister2 --fstal --s avgsubject --mgz
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Example 3: check that the average subject volume aligns with the
talairach subject:		 }}}
Checks that the average subject volume aligns with the talairach subject:
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  tkregister2 --fstal --s avgsubject --mgz == Example 4 ==
{{{
tkmedit avgsubject orig.mgz lh.white
}}}
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Example 4: check that the average subject surfaces align with the
volume:		 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.
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  tkmedit avgsubject orig.mgz lh.white = See Also =
[[make_average_volume]], [[make_average_surface]], [[recon-all]], [[make_final_surfaces]], [[morph_subject]]
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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

Index

Contents

  1. Name
  2. Description
  3. Synopsis
  4. Arguments
    1. Required Flagged Arguments
    2. Optional Flagged Arguments
  5. Examples
    1. Example 1
    2. Example 2
    3. Example 3
    4. Example 4
  6. See Also
  7. Reporting Bugs

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)