Hello creators of freesurfer,

 

I am trying to align my surfaces with DTI data and ultimately display them in Amira. I noticed that during the step mris_make_surfaces there is an orientation change from lh.orig to lh.white. I attached a snapshot of the two surfaces overlayed with my b0 data. You can see that the lh.orig (which is perfectly registered with b0) and lh.white files are not perfectly aligned but differ by some orientation change. Is there a way to undo this orientation change? Or perhaps output a text of shift so that I can change the coordinates in the surfaces?

 

The command is mris_make_surfaces –whiteonly –noaparc –mgz –T1 brain.finalsurfs subj_id lh

 

Thank you in advance for any guidance.

 

Sincerely,

 

Tina Jeon, M.S.

Biomedical Engineering Graduate Student

Dr. Hao Huang's Lab

Advanced Imaging Research Center

UT Southwestern Medical Center

(310) 592-1853