Hi Jamie,
it's impossible to judge surface accuracy from one slice. You need to move
forwards and back a couple of slices to see if the surface is curving
sharply out of plane.
Can you explain a bit more about what is unique about this volume? I
didn't really understand from your email. Is it a single subject MRI? Or
the average of some volumes processed using some nonlinear registration?
Bruce
On
Mon, 7 Apr 2008, Jamie Hanson wrote:
i think my attachment didn't make it through, the first time round.
example pics now attached.
thanks much,
jamie.
On Mon, Apr 7, 2008 at 1:10 PM, Jamie Hanson <[EMAIL PROTECTED]> wrote:
Hi Freesurfers-
I was trying to run freesurfer on a study template and was having
major problems with pial surface generation. Orig and Main surfaces
seem to be ok, but there are major missing chinks in pial surface.
Just to give some background, the template was being using for
Diffeomorphic Image Registration, so it is a very unique volume.I know
it is likely it is an intensity value issue.I wondered what folks have
done previously to correct similar issues?
It appears to be across a massive proportion of the brain, so
correcting by hand (by altering intensity values seems a bit labor
intensive and perhaps questionable in terms of reliability). I also
thought of trying to rerun some of the initial preprocessing
(autorecon1 + 2) with some more 'expert settings'. Initially, I was
running with no skull strip and no n3 flag (b/c the template has
already been skull-stripped and massive preprocessed), but was looking
for some additional advice and guidance.
Any thoughts or suggestions would be greatly appreciated.
Best,
jamie.
--
Jamie L. Hanson
Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab
University of Wisconsin - Madison
1500 Highland Avenue
Madison, WI 53706
***Please note my new email: [EMAIL PROTECTED]
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