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

-Deletions are marked like this.
+Additions are marked like this.
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-mri_label_volume - ??
+mri_label_volume
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-mri_label_volume volume1 voume2 f flo fhi
+mri_label_volume [options] <volume> <label 1> <label 2> ...
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-|| volume1 || ?? ||

|| volume2 || ??||

|| f || ??||

|| flo || ??||

|| fhi || ??||

== Required Flagged 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 ||
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-|| -a || ?? ||
+{{{

  -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

}}}
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+Line 44:
-= Outputs =

||??||



= Description =

??
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-mri_label_volume -a $SUBJECTS_DIR/mri/brain



= Bugs =

None



= See Also =



= Links =

FreeSurfer, FsFast



= Methods Description =

{{{??}}}



= References =
+{{{

set sdir=$SUBJECTS_DIR/subjid/mri

mri_label_volume -eTIV \

 $sdir/transforms/talairach.xfm 1948 \

 $sdir/aseg.mgz 17 53

}}}
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+Line 57: