Name

mri_label_volume

Synopsis

mri_label_volume [options] <volume> <label 1> <label 2> ...

Arguments

Positional Arguments

volume	the .mgz file, eg. aseg.mgz
label 1	the label number, eg. 17 (left hippocampus)
label 2	another label number, eg. 53 (right hippocampus)
...	more label numbers

Optional Flagged Arguments

  -pv <fname>   - compute partial volume effects using intensity volume <fname>
  -icv <fname>  - normalize by the intracranial volume in <fname>
  -s <subject>  - output in spreadsheet mode, including <subject> name in file
  -a            - compute volume of all non-zero voxels (e.g. for computing brain volume)
  -t <in> <out> - replace label <in> with label <out>. Useful for compute e.g. whole hippo vol
  -b <brain vol>- compute the brain volume from <brain vol> and normalize by it
  -p            - compute volume as a % of all non-zero labels
  -l <fname>    - log results to <fname>
  -atlas_icv <fname> <scalefactor> - specify LTA or XFM atlas transform file
  and scale factor to use for ICV correction (c.f. Buckner et al. 2004)
  -eTIV <fname> <scalefactor> - same as -atlas_icv
  -eTIV_matdat <fname> <scalefactor> <subject> - same as -eTIV,
  and generate matlab data appending <subject> to structure

Examples

set sdir=$SUBJECTS_DIR/subjid/mri
mri_label_volume -eTIV \
 $sdir/transforms/talairach.xfm 1948 \
 $sdir/aseg.mgz 17 53

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

BruceFischl