External Email - Use Caution

Re-posting to see if anyone has had this problem before and solutions they've implemented.

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/dc9pjj https://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