Hello Freesurfer Experts,

I have been trying to run mri_cvs_register to bring sub-millimeter data into MNI space, however the final outputs have large deformations to the brain. I have tried with both 0.5 mm and 0.7 mm using their respective sub-milimeter recons. It seems that the issue arises during Step 3(i) as the el_reg_tocvs_avg35_inMNI152.mgz does not have the deformations, but the step1_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz file does. Does anyone have any guidance on how I can troubleshoot this? 

I have attached the recon-all.log file for the 0.7 mm data. If you need me to share any other files, let me know. 

FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1

Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS

Thank you,

Noriana Jakopin