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 fischl@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.