I have successfully run a subject through recon-all --all using freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0. I am trying to spatially align and overlay rh.dpial.ribbon.mgz onto rawavg.mgz. Based on info from prior posts, I've tried the following commands:
mri_convert rh.dpial.ribbon.mgz -rl rawavg.mgz rh_dpial_ribbon_rawavespace.nii.gz
...and...
mri_vol2vol --mov rh.dpial.ribbon.mgz --targ rawavg.mgz --o rh_dpial_ribbon_rawavespace.nii.gz --regheader --interp nearest
These commands had identical outputs: the rh_dpial_ribbon_rawavespace.nii.gz file was in the same general orientation as rawavg.mgz, but misaligned. It looks like the rh.dpial.ribbon.mgz is in a different coordinate space than rawavg.mgz (i..e, not native), but I could not find documentation on which space that is, or where to find the transformation file(s) for it.
Could someone send me an example command for how to transform rh.dpial.ribbon.mgz into the same space as rawavg.mgz?
Thanks,
John