-- On Wed, 7 Apr 2010, Sherri Novis wrote: > 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 fischl@nmr.mgh.harvard.edu >> Sent: Apr 7, 2010 1:15 PM >> To: Sherri Novis echotalk@earthlink.net >> Cc: Sita Kakunoori sita@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 sita@nmr.mgh.harvard.edu >>>> Sent: Apr 7, 2010 12:55 PM >>>> To: Sherri Novis echotalk@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 > > >