Hi Noriana,
Do you have the log file from the cvs_registration itself? I assume that the recon for your data was successful.
Best, Lilla
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Noriana Jakopin <nejakopin1@gmail.com>
Sent: Thursday, September 3, 2020 1:45 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_cvs_register with sub-millimeter recons
 

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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