commands.txt

cd/projects/BICpipeline/Pipeline_Pilot/TestingFork/RSP_dev
export subjects='sub-2528'
export sessions='ses-A'
export SUBS_DIR=/data
export RSFCscripts=/scripts
export DATA=/data/derivatives/restingstatepipeline
export parcellation_labels_file=/scripts/aparc_labels_add.txt
export OUTPUT=/data/derivatives/restingstatepipeline/out

singularity run --bind ./scripts:/scripts --bind ../PEA_tutorial/BIDS:/data ./rsp.simg python2.7 /scripts/maskGen_dev
singularity run --bind ./scripts:/scripts --bind ../PEA_tutorial/BIDS:/data ./rsp.simg python2.7 /scripts/Freesurfer_ROIs_dev.py
singularity run --bind ./scripts:/scripts --bind ../PEA_tutorial/BIDS:/data ./rsp.simg /scripts/incorporate_suits4exp_dev.sh
singularity run --bind ./scripts:/scripts --bind ../PEA_tutorial/BIDS:/data --bind ./bxh_xcede_tools-1.11.14-lsb30.x86_64:/bxh ./rsp.simg /scripts/path3SUIT sub-2528/ses-A