That is a normal, if a somewhat ominous informational message. Matt.
From: <[email protected]> on behalf of Kavinash Loganathan <[email protected]> Date: Saturday, June 8, 2019 at 2:39 AM To: "[email protected]" <[email protected]> Subject: [HCP-Users] Strange output when running ./FreeSurferPipelineBatch.sh Hi guys, I finished the PreFreesurfer run on the example file and just started Freesurfer pipeline when I got this output: This script must be SOURCED to correctly setup the environment prior to running any of the other HCP scripts contained here 100307 About to use fsl_sub to queue or run /home/kavinash/projects/Pipelines/FreeSurfer/FreeSurferPipeline.sh set -- --subject=100307 --subjectDIR=/home/kavinash/projects/Pipelines_ExampleData/100307/T1w --t1=/home/kavinash/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore.nii.gz --t1brain=/home/kavinash/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore_brain.nii.gz --t2=/home/kavinash/projects/Pipelines_ExampleData/100307/T1w/T2w_acpc_dc_restore.nii.gz --printcom= . /home/kavinash/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh What does this mean? I think I sourced the correctly (its much the same as the Prefreesurfer file locations), but it doesn't openly say what error occurred. Attached the output file for the above run. Thanks in advance Kavinash [Image removed by sender.] _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
