run_luigi_pnlpipe.lsf

#!/bin/bash

# Copy this file to your project folder (usually called run.lsf), 
# edit as needed, and then start a cluster job by running: 
#     bsub < run_luigi_pnlpipe.lsf

# source pnlpipe3 environment
source /data/pnl/soft/pnlpipe3/bashrc3

# copy and edit /data/pnl/soft/pnlpipe3/luigi-pnlpipe/params/*/*.cfg
export LUIGI_CONFIG_PATH=/path/to/your/pipe_params.cfg

caselist=/path/to/caselist.txt
sessions=/path/to/sessions.txt

# replace NUM_CASES, NUM_PARALLEL, big-multi, and NUM_CORES variables as required by your data

#BSUB -J luigi-pnlpipe[1-NUM_CASES]%NUM_PARALLEL
#BSUB -o ~/luigi-pnlpipe-%J-%I.out
#BSUB -e ~/luigi-pnlpipe-%J-%I.err
#BSUB -q pri_pnl
#BSUB -R rusage[mem=8000]
#BSUB -n NUM_CORES


# run command
if [ -f ${caselist} ]
then
    # LSF script, list of subjects
    id=`head -${LSB_JOBINDEX} ${caselist} | tail -1`
else
    # shell script, one subject
    id=${caselist}
fi

/data/pnl/soft/pnlpipe3/luigi-pnlpipe/exec/ExecuteTask --task Freesurfer \
--bids-data-dir /data/pnl/DIAGNOSE_CTE_U01/rawdata \
--t1-template sub-*/ses-*/anat/*_T1w.nii.gz \
--t2-template sub-*/ses-*/anat/*_T2w.nii.gz \
-c ${id} \
-s ${sessions}