Thank you Bruce. I've had this prob randomly before - but recently it's been each of the last 10 datasets - so I think its a process issue that I introduced - but would love help from any direction.
If I use the upload site - which files to you need? will send wm.mgz, ?h.orig surface - any others? Thank you - Sherri -----Original Message----- >From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >Sent: Apr 7, 2010 1:15 PM >To: Sherri Novis <echot...@earthlink.net> >Cc: Sita Kakunoori <s...@nmr.mgh.harvard.edu>, freesurfer@nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Pial Surfaces Cutting off Gyri > >Hi Sherri, > >you may also have a topological defect near those control points, which >is causing the surfaces to lose the wm (and hence the gm also). What does >the wm.mgz look like there? Is the wm segmented correctly but not >included in the ?h.orig surface? If you upload this data we can take a >look, if you want. >Bruce > > >On Wed, 7 Apr 2010, Sherri Novis wrote: > >> 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 >> >> >> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
