Hi Jordan, I just had a similar discussion (off-list) with Nick recently. The distinction only matters if you end up trimming cerebellum voxels out of the aseg, and want your aseg for cerebellum to be correct.
Quoting Nick: "it [brain.finalsurfs.manedit.mgz] is used only in the instance (which has happened only once recently) where the pial surface extends into the cerebellum. in this case, you wouldnt want to trim away the cerebellum in brainmask.mgz, because then the cerebellum segmentation wont be correct in the aseg (or worst case the alignment to the atlas wont not be optimal). so we decided to add editing of brain.finalsurfs.manedit.mgz, since this is downstream of the aseg and is input to surface creation. End Quote Edits to brainmask.mgz still get applied, and if all you are doing is looking at cortical thickness, then you shouldn't need to do redo anything. cheers, -MH On Fri, 2011-11-18 at 11:55 -0800, Jordan Pierce wrote: > We've been manually editing brainmask.mgz to remove voxels that are > included in the pial surface that shouldn't be, and recently found on > the wiki that to remove cerebellum voxels we should be editing > brain.finalsurfs.manedit.mgz instead. What is the reason for this > difference? Do we need to redo edits that we've done only on > brainmask.mgz? We are going to be looking at cortical thickness. > > > Thanks, > > Jordan Pierce > Graduate Student > Behavioral and Brain Sciences Program > Psychology Department > The University of Georgia > _______________________________________________ > 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
