Hi Bruce, Running -autorecon2 -autorecon3 did not seem to fix the surfaces for this subject. Do you have any further suggestions on what we could try to correct the surfaces?
Thank you! Batool ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rizvi, Batool [br2...@cumc.columbia.edu] Sent: Wednesday, December 14, 2016 1:49 PM To: Freesurfer support list Subject: Re: [Freesurfer] incorrect pial surfaces after watershed adjustment Ohkay thanks, we'll go ahead and run autorecon2 and autorecon 3 on this subject then. Thanks! Batool ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, December 14, 2016 1:45 PM To: Freesurfer support list Subject: Re: [Freesurfer] incorrect pial surfaces after watershed adjustment Hi Batool if you need to change the watershed you will need to rerun everything from there forward. All of autorecon2 and autorecon3 I think at least cheers Bruce On Wed, 14 Dec 2016, Rizvi, Batool wrote: > > Hi FreeSurfer experts, > > > > We have a subject on which we had to do adjust the watershed parameters for, > since there was some > brain missing from the brainmask.mgz. The watershed itself worked, but after > that, we needed to > regenerate the surfaces after the bad skull strip was fixed, and we ran > "recon-all -autorecon-pial > -subjid <subject name>" > > > > That seemed to not work though, and it still shows that the surfaces do not > include the new brain > matter. Attached is an image of the output. Is there anything else we can try > to regenerate these > surfaces correctly? > > > > Thank you! > > Batool > > > _______________________________________________ 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
