You can extract a binary mask for any structure with mri_binarize --i aseg.mgz --match XX --o yourmask.mgh where XX is a number from $FREESURFER_HOME/FreeSurferColorLUT.txt (eg, 17 = left hippo) It is possible to generate hippo surfaces, but we cannot guarantee accuracy. Let me know if you want to know how. doug
Jie Shi wrote: > Hi, experts. We need to use FreeSurfer to process some analyze image > data. More specifically, we want to extract the hippocampus surfaces. > We know that FreeSurfer has done subcortical segmentation during > -autorecon2 stage in recon-all. We have checked the resulting aseg.mgz > file and found that it contains all substructures. So we wonder if > there is a way to get the separated .mgz files for each substructure > or could FreeSurfer generate the subcortical surfaces? Thanks a lot. > > Best, > Jie > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
