Index
Contents
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