I am attempting to align the GM mask (lh.ribbon.mgz) to the T1 in native space. I see this thread that states this command is the correct way:

mri_label2vol --seg lh.ribbon.mgz --temp rawavg.mgz --o ribbon-in-rawavg.mgz --regheader ribbon.mgz

from:http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33578.html

However, when I do do, the alignment is off. All of my rawavg.mgz are rotated relative to the original T1 in native space, so the GM masks are also not properly aligned. Is there a transformation that I am missing somewhere between rawavg.mgz and native T1?

Thank you,

Patrick