Hi Sneha can you send us some snapshots? Or upload the entire subject and we will take a look. You can always erase cerebellum from brain.finalsurfs and rerun recon3
cheers Bruce On Wed, 28 Jan 2015, Sneha Pandya wrote: > Hi Team, > > Can anyone please share if they have been successful in editing extending > pial to the cerebellum and which method has been successful in reference to > the email below. > > Thanks, > Sneha > > ____________________________________________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sneha Pandya > [snp2...@med.cornell.edu] > Sent: Tuesday, January 27, 2015 12:03 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Which command to use if pial extends to cerebellum > > Hi Team, > > I have few of my images in which pial surface extends to the cerebellum. > Please note that I have already made edits to the brainmask.mgz and have > already ran following command: > > recon-all -autorecon-pial -subjid subj > After lookin into several previous posts and freesurfer edit forum I came > across following solutions but its not clear which one to use when. Can > someone please shed a light to which recon command be used post making edits > to brain.finalsurfs.manedit.mgz for cerebellum and pial edits to > brainmask.mgz. I have also attached a screenshot for one of my case. > > recon-all -autorecon-pial -autorecon3 -subjid subj > OR > recon-all -make all -s subjid > OR > recon-all -all -clean-bm -s subjid > Thanks, > Sneha > > _______________________________________________ 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.
