Index

Contents

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

Name

make_average_volume

Description

Synopsis

make_average_volume [options] --subjects subjects --fsgd fsgdfile

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'

--topdir topdir

Put data here and link to SUBJECTS_DIR

--xform xform

Use mri/transforms/xformname (default is talairach.xfm

--sdir <SUBJECTS_DIR to use instead of the one in the env>

--sd

Same as --sdir

--force

Overwrite existing average subject data

--keep-all-orig

Concatenate all orig vols into mri/orig.all.mgz

--no-aseg

Do not create 'average' aseg

--nocleanup

Do not delete temporary files

--help

Short descriptive help

--version

Script version info

--echo

Enable command echo, for debugging

--debug

Same as --echo

Examples

make_average_volume --out avgsubject --subjects subj1 subj2 subj3 subj4

This will create $SUBJECTS_DIR/avgsubject with orig.mgz, brain.mgz, and T1.mgz which will be averages of subjects 1-4.

See Also

recon-all, make_final_surfaces, morph_subject

Reporting Bugs

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