| Deletions are marked like this. | Additions are marked like this. |
| Line 28: | Line 28: |
|
{{{ -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 }}} |
||-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|| |
Index
Contents
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>