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
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