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Hi Freesurfer support,
Recently, I submitted a script to run recon-all on 100 mri images on UCSD's computing cluster, called EXPANSE. I get an error file that says "nu_correct: Command not found. FREESURFER: Undefined variable." The sample error file and the output file I have attached for one of the subjects are recon-all-slurm.29376886.exp-5-44.err & recon-all-slurm.29376886.exp-5-44.out respectively. The script I used to submit the job via slurm is called recon-all-slurm.sb.
I googled the error and found that someone else who had a similar situation did not source their Freesurfer environment correctly. Would this be the same thing for us as well? The main thing for us is Freesurfer/7.2.0 already has been available as a module for us on EXPANSE.
Sincerely,
Yilei