Hi Karteek the aseg isn't surface based, sorry, but the watershed that we use to do the skull stripping is and does use smoothness constraints. If it is leaving dura around try using mri_gcut.
cheers Bruce On Thu, 18 May 2017, Karteek Popuri wrote: > Hi, > My goal is to use the best possible skull-stripped version of the input MRI. > Is brainmask.mgz the one? or I was wondering if anyone has tried improving > the brainmask.mgz further by masking it out using the aseg.mgz. Will that > help with regards to getting rid of the dura in the brainmask.mgz. My > intuition is because the generation of aseg.mgz includes a surface-based > algorithm, the smoothing constraints of the surface evolution should minimize > the "leakage" of the GM surface into the dura, hence the aseg might have some > dura but not as much as the brainmask. Will be thankful for any > suggestions/comments. > Karteek > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ 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.
