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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
