Name

mri_aparc2aseg - Maps the cortical labels from the automatic cortical parcellation (aparc) to the automatic segmentation volume (aseg). The result can be used as the aseg would.

Synopsis

mri_aparc2aseg [ options ]

Arguments

Required Flagged Arguments

--s argSubject

subject

recon-ed subject in the SUBJECTS_DIR

Optional Flagged Arguments

--o argOutput	output file	output the segmentation volume (relative to the current dir)
--a2005	use aparc.a2005 instead of aparc
--ribbon	use mri/hemi.ribbon.mgz as a mask for the cortex
--annot argName	use specified label file instead of aparc
--version	display version	show version information and exit

Outputs

volume1

segmentation volume

Description

Maps the cortical labels from the automatic cortical parcellation (aparc) to the automatic segmentation volume (aseg). The result can be used as the aseg would. The algorithm is to find each aseg voxel labeled as cortex (3 and 42) and assign it the label of the closest cortical vertex. If the voxel is not in the ribbon (as defined by mri/lh.ribbon and rh.ribbon), then the voxel is marked as unknown (0). This can be turned off with --noribbon. The cortical parcellation is obtained from subject/label/hemi.aparc.annot which should be based on the curvature.buckner40.filled.desikan_killiany.gcs atlas. The aseg is obtained from subject/mri/aseg.mgz and should be based on the RB40_talairach_2005-07-20.gca atlas. If these atlases are used, then the segmentations can be viewed with tkmedit and the FreeSurferColorLUT.txt color table found in $FREESURFER_HOME. These are the default atlases used by recon-all.

Examples

Example 1

mri_aparc2aseg --s bert
tkmedit bert orig.mgz -segmentation mri/aparc+aseg.mgz \
   $FREESURFER_HOME/FreeSurferColorLUT.txt

Computes the aparc+aseg.mgz volume for subject bert.

Reporting Bugs

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

Author/s

Doug Greve