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
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
FreeSurferPipeline.sh.o22279
Description: Binary data
