Can you send the recon-all.log file?
On 6/18/2021 10:54 AM, Soichi Hayashi wrote:
External Email - Use Caution
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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