#!/bin/bash

#$ -V

#$ -cwd

#$ -S /bin/bash

#$ -N fmriprep

#$ -o logs/fmriprep/subject_$TASK_ID.out

#$ -e logs/fmriprep/subject_$TASK_ID.out

#$ -m be -M jacob.taylor.fisher@gmail.com

#$ -q omni

#$ -pe mpi 36

#$ -P quanah

#$ -t 20

module load singularity

export SINGULARITYENV_FS_LICENSE=$HOME/.licenses/freesurfer/license.txt

singularity run --cleanenv my_images/fmriprep-latest.simg bids_nii preproc participant --participant-label $(printf %02d $SGE_TASK_ID) --nthreads 36 --fs-no-reconall --fd-spike-threshold .5 --use-aroma -w preproc/fmriprep_work