Hi Michael and Matt, if I'm interpreting the output correctly, the “$var” resolve as following: "$SubjectID" --->
--subject=VIMS_HC_034 "$SubjectDIR" ---> --subjectDIR=/home/lisak/Desktop/NMDA_HCP/controls/VIMS_HC_034/T1w "$T1wImage" ---> there are actually two things here --t1=/home/lisak/Desktop/NMDA_HCP/controls/VIMS_HC_034/T1w/T1w_acpc_dc_restore.nii.gz and --t1brain=/home/lisak/Desktop/NMDA_HCP/controls/VIMS_HC_034/T1w/T1w_acpc_dc_restore_brain.nii.gz "$T2wImage" ---> --t2=/home/lisak/Desktop/NMDA_HCP/controls/VIMS_HC_034/T1w/T2w_acpc_dc_restore.nii.gz There is also an additional thing shown after T2 in the output, which might be related, --printcom= and then in a new line . /home/lisak/Desktop/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh which is where the analysis stops/breaks off and moves on to a new participant. I will not be back in the lab until Monday, so I won't be able to check anything directly before then. As for the editors, I only use gedit, and having done a google search, it seems to automatically highlight scripts which language it recognizes. Not sure if that's what it looks like, but certain parts of the script on my lab computer are blue, others are pink, others are gray-ish etc. So I guess they're highlighted? I can deliberately remove a quote on Monday and see if it changes anything appearance-wise. I'll keep you updated. Best, Darko _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
