cd $SUBJECTS_DIR/subject/surf mri_tesselate ../mri/aseg.mgz 17 lh.hippocampus; # this generates a surface with jagged edges mris_smooth -nw -n 10 lh.hippocampus lh.hippocampus.sm10; # smooths surface 10 smoothing steps is just a guess
# Visusalize the surface tksurfer subject lh hippocampus.sm10 # See the surface overlaid on the volume tkmedit subject orig.mgz lh.hippocampus.sm10 -aseg Not that when you run the tkmedit/tksurfer commands, they will complain that the surface does not match. This is not a problem for this application. doug Jie Shi wrote: > Hi, thank you very much. Actually we do want to know how to get the > surfaces in order to compare with ours. > > Jie > > > On Wed, Nov 9, 2011 at 4:59 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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 > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > -- 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
