Dear All,
Please advise. Some of the dural enclosure defects involve both wm and pia surfaces (wm/pia extending to dura), so in those cases, correcting pia will also touch the wm. Editing wm in wm.mgz and running recon-all -autorecon2-wm -autorecon3 ameliorates but does not solve the wm defect issue (some wm in some places still extending (albeit less) outside to encompass some dural segments). At this point, to options I see are: - to edit brainmask.mgz for pial surface, but because wm will be touched by this correction, to run the whole -autorecon2 -autorecon 3 - to edit brain.finalsurfs.mgz for pial, then run -autorecon -pial, but I do not know what this does to wm since wm is upstream. Thank you, Octavian On Fri, Mar 10, 2017 at 9:51 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Octavian > > if you want to regenerate the pial surface you have to run autorecon3 also. > > And I don't think you want to edit the wm.mgz for wm edits. Probably you > should edit brain.finalsurfs.mgz for both wm and pial. Can someone who has > done more recent recons than I have confirm this? > > cheers > Bruce > > > > On Thu, 9 Mar 2017, Octavian Lie wrote: > > Dear All, >> >> A simple issue of precedence. In the recon-all pipeline, wm edits take >> precedence to pial edits. >> If there are both wm and pial defects, should one apply edits >> sequentially, >> say on brainmask.mgz (first wm edits, rerun recon-all say recon-all >> -autorecon2 -wm, then do pial edits, rerun recon-all say recon-all >> -autorecon2 -pial) or to some extent pial edits influence the final >> surface >> generation in conjunction to wm edits (understood that the latter may >> influence more the final form than the former -pial- edits), in that case >> one may do both edits, then run -autorecon2 -wm only. >> >> Please advise, >> Octavian >> >> > _______________________________________________ > 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. > >
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