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@@ -52,7 +52,7 @@ fi
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# maximum number of cpus per process:
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# maximum number of cpus per process:
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N_CPUS=1
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N_CPUS=1
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# memory demand in *GB*
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# memory demand in *GB*
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-MEM_GB=5
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+MEM_GB=6
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# memory demand in *MB*
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# memory demand in *MB*
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MEM_MB="$((${MEM_GB} * 1000))"
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MEM_MB="$((${MEM_GB} * 1000))"
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# read subject ids from the list of the text file
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# read subject ids from the list of the text file
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@@ -92,13 +92,13 @@ for SUB in ${SUB_LIST}; do
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# request multiple cpus
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# request multiple cpus
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echo "#SBATCH --cpus-per-task ${N_CPUS}" >> job
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echo "#SBATCH --cpus-per-task ${N_CPUS}" >> job
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# write output and error log to log folder:
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# write output and error log to log folder:
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- echo "#SBATCH --output ${PATH_LOGS}/slurm-%j.out" >> job
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+ echo "#SBATCH --output ${PATH_LOGS}/slurm-heudiconv-%j.out" >> job
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# email notification on abort/end, use 'n' for no notification:
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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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echo "#SBATCH --mail-type NONE" >> job
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# set working directory
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# set working directory
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echo "#SBATCH --workdir ." >> job
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echo "#SBATCH --workdir ." >> job
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# define the heudiconv command:
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# define the heudiconv command:
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- echo "singularity run -B ${PATH_INPUT}:/input:ro \
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+ echo "singularity run --contain -B ${PATH_INPUT}:/input:ro \
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-B ${PATH_OUTPUT}:/output:rw -B ${PATH_CODE}:/code:ro \
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-B ${PATH_OUTPUT}:/output:rw -B ${PATH_CODE}:/code:ro \
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${PATH_CONTAINER} -d /input/${DICOM_DIR_TEMPLATE} -s ${SUB} \
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${PATH_CONTAINER} -d /input/${DICOM_DIR_TEMPLATE} -s ${SUB} \
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--ses ${SES_PAD} -o /output -f /code/${HEURISTIC_FILE} \
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--ses ${SES_PAD} -o /output -f /code/${HEURISTIC_FILE} \
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