Index

Name

mri_label_volume - get various volume stats

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

mri_label_volume (last edited 2009-02-12 16:37:34 by NickSchmansky)