afni.nimh.nih.gov

Hi Peter,
Thanks for the info. I was actually interested more in a hybrid approach and he second option which is running a surface based analysis for cortical regions as well as volumentric analysis for subcortical regions.

I wanted to take my native space brains and warp to MNI space. 3dQwarp does an exceptional job for subcortical regions and I wanted to take advantage of surface gyri information for accurately warping surfaces to the MNI surface template I am creating. I think mine would be more of a hybrid approach or at least in some fashion use the surface information for fixing the warps cortically.

In terms of the afni_proc.py -spec function, is the aligment similar to bbregister where it does a boundary based alignment and the cost function mitigates areas susceptible to high B0 inhomogeneity?

Thanks,
Ajay