pycap_run_hcp_step3_Ssplit.sh

#!/bin/bash
#SBATCH -J St3_P100
#SBATCH --mem-per-cpu=8G
#SBATCH --cpus-per-task=2
#SBATCH --partition=pi_anticevic
#SBATCH --time=1-00:00:00
#SBATCH --output="/Studies/CAP_Time_Analytics/cap_codes/slurm_output/St3_P100-%A_%a.out"
#SBATCH --array=1-1000

module load miniconda
source activate /software/env/pycap_env


perm=$SLURM_ARRAY_TASK_ID
Pth=100

basedir=/Studies/


homedir=$basedir/Connectome/subjects/
outdir=$basedir/CAP_Time_Analytics/results/Ssplit$perm/
datadir=$basedir/CAP_Time_Analytics/groupdata/Ssplit$perm/
pscalarfilen=$basedir/Connectome/Parcellations/CABNP/CortexSubcortex_ColeAnticevic_NetPartition_wSubcorGSR_parcels_LR_ReorderedByNetworks_Zeroes.pscalar.nii
sublistfilen=$basedir/CAP_Time_Analytics/sublist/hcp_n337.csv


python $basedir/CAP_Time_Analytics/cap_codes/pyCAP/pyCAP/pycap_Ssplit_run_hcp_step3_trt.py \
--homedir $homedir \
--outdir $outdir \
--datadir $datadir \
--sublistfilen $sublistfilen \
--pscalarfilen $pscalarfilen \
--perm $perm \
--gsr y \
--unit p \
--seedtype seedfree \
--randTthreshold $Pth \
--scrubbing y \
--runorder 2134 \
--motiontype fd \
--motionthreshold 0.5 \
--motiondisplay n \
--ndummy 100