|
|
@@ -0,0 +1,119 @@
|
|
|
+#!/usr/bin/bash
|
|
|
+# ==============================================================================
|
|
|
+# SCRIPT INFORMATION:
|
|
|
+# ==============================================================================
|
|
|
+# SCRIPT: CREATE PARTICIPANT-LEVEL MRIQC REPORTS FOR A BIDS-STRUCTURED DATASET
|
|
|
+# PROJECT: HIGHSPEED
|
|
|
+# WRITTEN BY LENNART WITTKUHN, 2018 - 2020
|
|
|
+# CONTACT: WITTKUHN AT MPIB HYPHEN BERLIN DOT MPG DOT DE
|
|
|
+# MAX PLANCK RESEARCH GROUP NEUROCODE
|
|
|
+# MAX PLANCK INSTITUTE FOR HUMAN DEVELOPMENT (MPIB)
|
|
|
+# MAX PLANCK UCL CENTRE FOR COMPUTATIONAL PSYCHIATRY AND AGEING RESEARCH
|
|
|
+# LENTZEALLEE 94, 14195 BERLIN, GERMANY
|
|
|
+# ACKNOWLEDGEMENTS: THANKS TO ALEXANDER SKOWRON AND NIR MONETA @ MPIB FOR HELP
|
|
|
+# ==============================================================================
|
|
|
+# DEFINE ALL PATHS:
|
|
|
+# ==============================================================================
|
|
|
+# path to the base directory:
|
|
|
+PATH_BASE="${HOME}"
|
|
|
+# path to the project root directory
|
|
|
+PATH_ROOT="${PATH_BASE}/highspeed"
|
|
|
+# define the name of the project:
|
|
|
+PROJECT_NAME="highspeed-mriqc"
|
|
|
+# define the path to the project folder:
|
|
|
+PATH_PROJECT="${PATH_ROOT}/${PROJECT_NAME}"
|
|
|
+# define the name of the current task:
|
|
|
+TASK_NAME="mriqc"
|
|
|
+# define the path to the script main directory:
|
|
|
+PATH_CODE="${PATH_PROJECT}/code"
|
|
|
+# cd into the directory of the current task:
|
|
|
+cd "${PATH_CODE}"
|
|
|
+# define the path to the singularity container:
|
|
|
+PATH_CONTAINER="${PATH_PROJECT}/tools/${TASK_NAME}/${TASK_NAME}_0.15.2rc1.sif"
|
|
|
+# define the path for the templateflow cache
|
|
|
+PATH_TEMPLATEFLOW="${PATH_BASE}/.cache/templateflow"
|
|
|
+# path to the data directory (in bids format):
|
|
|
+PATH_INPUT="${PATH_PROJECT}/bids"
|
|
|
+# path to the output directory:
|
|
|
+PATH_OUTPUT=${PATH_PROJECT}
|
|
|
+# path to the working directory:
|
|
|
+PATH_WORK=${PATH_PROJECT}/work
|
|
|
+# path to the log directory:
|
|
|
+PATH_LOG=${PATH_PROJECT}/logs/$(date '+%Y%m%d_%H%M%S')
|
|
|
+# path to the text file with all subject ids:
|
|
|
+PATH_SUB_LIST="${PATH_CODE}/highspeed-participant-list.txt"
|
|
|
+# ==============================================================================
|
|
|
+# CREATE RELEVANT DIRECTORIES:
|
|
|
+# ==============================================================================
|
|
|
+# create output directory:
|
|
|
+if [ ! -d ${PATH_OUTPUT} ]
|
|
|
+then
|
|
|
+ mkdir -p ${PATH_OUTPUT}
|
|
|
+fi
|
|
|
+# create working directory:
|
|
|
+if [ ! -d ${PATH_WORK} ]
|
|
|
+then
|
|
|
+ mkdir -p ${PATH_WORK}
|
|
|
+fi
|
|
|
+# create directory for log files:
|
|
|
+if [ ! -d ${PATH_LOG} ]
|
|
|
+then
|
|
|
+ mkdir -p ${PATH_LOG}
|
|
|
+else
|
|
|
+ # remove old log files inside the log container:
|
|
|
+ rm -r ${PATH_LOG}/*
|
|
|
+fi
|
|
|
+# ==============================================================================
|
|
|
+# DEFINE PARAMETERS:
|
|
|
+# ==============================================================================
|
|
|
+# maximum number of cpus per process:
|
|
|
+N_CPUS=5
|
|
|
+# memory demand in *GB*
|
|
|
+MEM_GB=9
|
|
|
+# read subject ids from the list of the text file:
|
|
|
+SUB_LIST=$(cat ${PATH_SUB_LIST} | tr '\n' ' ')
|
|
|
+# declare an array with sessions you want to run:
|
|
|
+declare -a SESSIONS=("01" "02")
|
|
|
+#for SUB in ${SUB_LIST}; do
|
|
|
+# ==============================================================================
|
|
|
+# RUN MRIQC:
|
|
|
+# ==============================================================================
|
|
|
+# initilize a subject counter:
|
|
|
+SUB_COUNT=0
|
|
|
+for SUB in ${SUB_LIST}; do
|
|
|
+ # update the subject counter:
|
|
|
+ let SUB_COUNT=SUB_COUNT+1
|
|
|
+ # create the subject number with zero-padding:
|
|
|
+ SUB_PAD=$(printf "%02d\n" ${SUB_COUNT})
|
|
|
+ # loop over all sessions:
|
|
|
+ for SES in ${SESSIONS[@]}; do
|
|
|
+ # create a new job file:
|
|
|
+ echo "#!/bin/bash" > job
|
|
|
+ # name of the job
|
|
|
+ echo "#SBATCH --job-name mriqc_sub-${SUB_PAD}_ses-${SES}" >> job
|
|
|
+ # add partition to job
|
|
|
+ echo "#SBATCH --partition gpu" >> job
|
|
|
+ # set the expected maximum running time for the job:
|
|
|
+ echo "#SBATCH --time 24:00:00" >> job
|
|
|
+ # determine how much RAM your operation needs:
|
|
|
+ echo "#SBATCH --mem ${MEM_GB}GB" >> job
|
|
|
+ # email notification on abort/end, use 'n' for no notification:
|
|
|
+ echo "#SBATCH --mail-type NONE" >> job
|
|
|
+ # write log to log folder:
|
|
|
+ echo "#SBATCH --output ${PATH_LOG}/slurm-%j.out" >> job
|
|
|
+ # request multiple cpus:
|
|
|
+ echo "#SBATCH --cpus-per-task ${N_CPUS}" >> job
|
|
|
+ # export template flow environment variable:
|
|
|
+ echo "export SINGULARITYENV_TEMPLATEFLOW_HOME=/templateflow" >> job
|
|
|
+ # define the main command:
|
|
|
+ echo "singularity run -B ${PATH_INPUT}:/input:ro \
|
|
|
+ -B ${PATH_OUTPUT}:/output:rw -B ${PATH_WORK}:/work:rw \
|
|
|
+ -B ${PATH_TEMPLATEFLOW}:/templateflow:rw \
|
|
|
+ ${PATH_CONTAINER} /input/ /output/ participant --participant-label ${SUB_PAD} \
|
|
|
+ --session-id ${SES} -w /work/ --verbose-reports --write-graph \
|
|
|
+ --n_cpus ${N_CPUS} --mem_gb ${MEM_GB} --no-sub" >> job
|
|
|
+ # submit job to cluster queue and remove it to avoid confusion:
|
|
|
+ sbatch job
|
|
|
+ rm -f job
|
|
|
+ done
|
|
|
+done
|
Lennart Wittkuhn