Can you send the recon-all.log file?
On 6/18/2021 10:54 AM, Soichi Hayashi wrote:
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Hello. I am having a problem running freesurfer on a HCP 7T data and I am wondering if someone from this mail list could help me out.
I am trying to run freesurfer (v7.1.1) and I am seeing the following error message.
ERROR! FOV=268.800 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible.
I am already passing -cw256 option.
$ recon-all -i ../60ccadb32b8bed7302843abc/59a09e1d34ea2464e4d1bdcd/t1.nii.gz -subject output -all -parallel -openmp 8 -hires -cw256 -expert expert.opts
The error message sounds like my -cw256 option is ignored, but I am not sure.. I see this at the top of the stdout log.
INFO: hi-res volumes are conformed to the min voxel size Subject Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Current Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 INFO: SUBJECTS_DIR is /export/prod/60ccadb32b8bed493f843abb/60ccadbb2b8bed6894843ac0 Actual FREESURFER_HOME /usr/local/freesurfer Linux slurm9-compute3 4.15.0-126-generic #129-Ubuntu SMP Mon Nov 23 18:53:38 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/export/prod/60ccadb32b8bed493f843abb/60ccadbb2b8bed6894843ac0/output/scripts/recon-all.local-copy' -cw256 option is now persistent (remove with -clean-cw256) /export/prod/60ccadb32b8bed493f843abb/60ccadbb2b8bed6894843ac0/output
I believe "-cw256 option is now persistent" means that freesurfer is aware that I am setting this parameter?
expert.opts is empty.
I appreciate if you could assist me in troubleshooting this error message!
Soichi
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