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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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