And in your second set of images, you probably need to edit the wm.mgz. I suspect that there is a topology problem that is messing up the wm.orig
cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu On 10/17/12 12:46 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Jon > >usually this happens because the wm in the wm.mgz doesn't extend out far >enough. Is that the case here? If not, you can also try direct >repositioning in freeview under tools->reposition surface. > >cheers >Bruce > >p.s. we also have some newer tools that I've been working on that can use >a >flair or T2 image for this purpose, if you happen to have a high res one > >On Wed, 17 Oct 2012, Jonathan Holt wrote: > >> I'm wondering about how to best approach two similar problems with pial >> surfaces. In one case I'd like to extend it and in the other I'd like to >> reduce it (for lack of a better term)These first two images are from a >>brain >> in which I'd like to extend the surface. >> >> http://i.imgur.com/ziDQd.png >> http://i.imgur.com/i0sX3.png >> >> In this case focus on the bottom left and right corners of the cortex. >>You >> can see, especially in the second image (with aseg.mgz loaded), the pial >> surface cuts off part of the cortex on both sides. Interestingly, the >>pial >> surface seems to adhere to the aparc.mgz file, which is loaded and >>pretty >> clear in the first image, where the left out parts of the cortex are >>just >> labelled as 'none'. >> >> http://i.imgur.com/aUKiG.png >> http://i.imgur.com/4BRwv.png >> >> In the second case I want to edit the pial surface so it follows that >>gyrus >> toward the midline in the left hemisphere. In this case I've tried >>control >> points, specifically along the gyrus, and autorecon2-cp. I also tried to >> edit the parcellation along the gyrus for several slides followed by >> autorecon2 & 3. This didn't help anything, so I'm a bit stuck. You can >>see >> this brain follows the same trend as the last in which the pial surface >> follows the aparc.mgz, and the aseg.mgz seems more or less correct. >> >> Thanks and any help would be awesome! >> >> jon >> >>_______________________________________________ >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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
