There is an error in your first 'recon-all -autorecon1 -noskullstrip' attempt: " \n**************************************** ERROR! FOV=302.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. ****************************************\n "

You can't run recon-all '-autorecon2 -autorecon3' until you have successfully run autorecon1.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Michal Zamberg-Elad Sent: Wednesday, May 15, 2024 7:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] error using mri_em_register

External Email - Use Caution It does not create the nu.mgz file.

Error logs are attached. The result is that when running recon all it cannot find the LH and RH files and then collapses.

Darwin Kernel Version 21.3.0 iMac-Pro 21.3.0 Root: xnu-8019.80.24~20/RELEASE_X86_64 x86_64

Thank you, Michal