Thanks Sita. I have struggled with how to capture very ghostly gray matter. Sometimes throwing a CP in it works (I understand now this may be hosing it sometimes) - if AR2-cp w/CPs in white matter is not driving the pial surfaces to capture all the gray - is the only way to capture the ghostly gray matter to directly edit the pial surface?
I was trying to avoid that. I was told don't ever edit the pial surfaces - not sure why though. Will manual edits of the pial surfaces cause other problems in getting surface segmentation stats? Thank you - Sherri -----Original Message----- >From: Sita Kakunoori <s...@nmr.mgh.harvard.edu> >Sent: Apr 7, 2010 12:55 PM >To: Sherri Novis <echot...@earthlink.net> >Cc: freesurfer@nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Pial Surfaces Cutting off Gyri > > >Hi Sherri, > >one of the control points seems to be in gray matter, which is probably >causing this. Please try deleting it and rerunning autorecon2-cp. > >Sita. > > >On Tue, 6 Apr 2010, Sherri Novis wrote: > >> Hello brilliant and generous FS people, >> >> I have introduced a problem I cannot solve. I am simply trying to capture >> as much gray matter as possible. We have some very bad constrast images >> (ghostly edeges where the gray matter should be). I'm adding control points >> to try to capture - however, now when I run AR2-cp, the pial surfaces go >> haywire on the superior borders of the slices. >> >> Attached are two images displaying the problem. >> >> I have edited wm.mgz to fill in the ventricles because I was getting >> islands, and I manually edited the brainmask to remove some vasculature that >> was being included in the pial surfaces. >> >> Can you tell me where I introduced this instability? >> >> Best Regards, >> Sherri > > >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
