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+#!/usr/bin/bash
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+# ==============================================================================
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+# SCRIPT INFORMATION:
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+# ==============================================================================
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+# SCRIPT: RUN FMRIPREP ON THE MPIB CLUSTER (TARDIS)
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+# PROJECT: HIGHSPEED
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+# WRITTEN BY LENNART WITTKUHN, 2018 - 2020
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+# CONTACT: WITTKUHN AT MPIB HYPHEN BERLIN DOT MPG DOT DE
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+# MAX PLANCK RESEARCH GROUP NEUROCODE
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+# MAX PLANCK INSTITUTE FOR HUMAN DEVELOPMENT
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+# MAX PLANCK UCL CENTRE FOR COMPUTATIONAL PSYCHIATRY AND AGEING RESEARCH
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+# LENTZEALLEE 94, 14195 BERLIN, GERMANY
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+# ACKNOWLEDGEMENTS: THANKS HRVOJE STOJIC (UCL) AND ALEX SKOWRON (MPIB) FOR HELP
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+# ==============================================================================
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+# DEFINE ALL PATHS:
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+# ==============================================================================
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+# path to the base directory:
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+PATH_BASE="${HOME}"
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+# path to the project root directory
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+PATH_ROOT="${PATH_BASE}/highspeed"
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+# define the name of the project:
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+PROJECT_NAME="highspeed-fmriprep"
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+# define the path to the project folder:
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+PATH_PROJECT="${PATH_ROOT}/${PROJECT_NAME}"
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+# define the name of the current task:
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+TASK_NAME="fmriprep"
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+# path to the current shell script:
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+PATH_CODE=${PATH_PROJECT}/code
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+# cd into the directory of the current script:
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+cd "${PATH_CODE}/${TASK_NAME}"
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+# path to the fmriprep ressources folder:
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+PATH_FMRIPREP=${PATH_PROJECT}/tools/${TASK_NAME}
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+# path to the fmriprep singularity image:
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+PATH_CONTAINER=${PATH_FMRIPREP}/${TASK_NAME}_1.2.2.sif
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+# path to the freesurfer license file on tardis:
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+PATH_FS_LICENSE=${PATH_FMRIPREP}/fs_600_license.txt
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+# path to the data directory (in bids format):
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+PATH_BIDS=${PATH_PROJECT}//bids
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+# path to the output directory:
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+PATH_OUT=${PATH_PROJECT}
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+# path to the freesurfer output directory:
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+PATH_FREESURFER="${PATH_OUT}/freesurfer"
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+# path to the working directory:
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+PATH_WORK=${PATH_PROJECT}/work
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+# path to the log directory:
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+PATH_LOG=${PATH_PROJECT}/logs/$(date '+%Y%m%d_%H%M%S')
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+# path to the text file with all subject ids:
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+PATH_SUB_LIST="${PATH_CODE}/fmriprep/highspeed-participant-list.txt"
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+# ==============================================================================
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+# CREATE RELEVANT DIRECTORIES:
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+# ==============================================================================
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+# create output directory:
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+if [ ! -d ${PATH_OUT} ]; then
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+ mkdir -p ${PATH_OUT}
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+fi
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+# create freesurfer output directory
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+if [ ! -d ${PATH_FREESURFER} ]; then
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+ mkdir -p ${PATH_FREESURFER}
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+fi
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+# create directory for work:
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+if [ ! -d ${PATH_WORK} ]; then
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+ mkdir -p ${PATH_WORK}
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+fi
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+# create directory for log files:
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+if [ ! -d ${PATH_LOG} ]; then
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+ mkdir -p ${PATH_LOG}
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+fi
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+# ==============================================================================
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+# DEFINE PARAMETERS:
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+# ==============================================================================
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+# maximum number of cpus per process:
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+N_CPUS=8
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+# maximum number of threads per process:
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+N_THREADS=8
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+# memory demand in *GB*
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+MEM_GB=35
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+# memory demand in *MB*
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+MEM_MB="$((${MEM_GB} * 1000))"
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+# user-defined subject list
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+PARTICIPANTS=$1
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+# check if user input was supplied:
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+if [ -z "$PARTICIPANTS" ]; then
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+ echo "No participant label supplied."
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+ # read subject ids from the list of the text file
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+ SUB_LIST=$(cat ${PATH_SUB_LIST} | tr '\n' ' ')
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+else
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+ SUB_LIST=$PARTICIPANTS
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+fi
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+# ==============================================================================
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+# RUN FMRIPREP:
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+# ==============================================================================
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+# initalize a subject counter:
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+SUB_COUNT=0
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+# loop over all subjects:
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+for SUB in ${SUB_LIST}; do
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+ # update the subject counter:
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+ let SUB_COUNT=SUB_COUNT+1
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+ # get the subject number with zero padding:
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+ SUB_PAD=$(printf "%02d\n" $SUB_COUNT)
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+ # create participant-specific working directory:
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+ PATH_WORK_SUB="${PATH_WORK}/sub-${SUB_PAD}"
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+ if [ ! -d ${PATH_WORK_SUB} ]; then
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+ mkdir -p ${PATH_WORK_SUB}
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+ fi
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+ # create a new job file:
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+ echo "#!/bin/bash" > job
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+ # name of the job
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+ echo "#SBATCH --job-name fmriprep_sub-${SUB_PAD}" >> job
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+ # add partition to job
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+ echo "#SBATCH --partition gpu" >> job
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+ # set the expected maximum running time for the job:
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+ echo "#SBATCH --time 40:00:00" >> job
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+ # determine how much RAM your operation needs:
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+ echo "#SBATCH --mem ${MEM_GB}GB" >> job
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+ # email notification on abort/end, use 'n' for no notification:
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+ echo "#SBATCH --mail-type NONE" >> job
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+ # write log to log folder
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+ echo "#SBATCH --output ${PATH_LOG}/slurm-fmriprep-%j.out" >> job
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+ # request multiple cpus
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+ echo "#SBATCH --cpus-per-task ${N_CPUS}" >> job
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+ # define the fmriprep command:
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+ echo "singularity run --cleanenv -B ${PATH_BIDS}:/input:ro \
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+ -B ${PATH_OUT}:/output:rw -B ${PATH_FMRIPREP}:/utilities:ro \
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+ -B ${PATH_FREESURFER}:/output/freesurfer:rw \
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+ -B ${PATH_WORK_SUB}:/work:rw ${PATH_CONTAINER} \
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+ --fs-license-file /utilities/fs_600_license.txt \
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+ /input/ /output/ participant --participant_label ${SUB_PAD} -w /work/ \
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+ --mem_mb ${MEM_MB} --nthreads ${N_CPUS} --omp-nthreads $N_THREADS \
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+ --write-graph --stop-on-first-crash \
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+ --output-space T1w fsnative template fsaverage \
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+ --notrack --verbose --resource-monitor" >> job
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+ # submit job to cluster queue and remove it to avoid confusion:
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+ sbatch job
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+ rm -f job
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+done
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Lennart Wittkuhn