Hi Freesurfer team,
We’re having some trouble with the T2pial option. We are currently getting the Martinos Center ABCD project Tisdall/van der Kouwe vNav MPRAGE and T2SPACE at 0.8mm^3, bandwidth matched for distortion.
Linked below are 2 gifs were we have found areas we thought the T2 and –T2pial option would help differentiate brain from non-brain:
https://goo.gl/dc9pjjhttps://goo.gl/AsCCbA
I’ve read the discussion by Bruce, Matt, and Antonin about altering the final lh/rh mris_make_surface command with the T2. Has anyone found more optimal numbers for the nsigma_above and nsigma_below arguments?
Is there anything else I could try to get this working better?
Thanks!
-Adam