From c359938776b9c6da138d15502abaed72097836e6 Mon Sep 17 00:00:00 2001 From: McKenzie Paige Hagen <35019015+mckenziephagen@users.noreply.github.com> Date: Tue, 10 Sep 2024 10:32:53 -0700 Subject: [PATCH 1/2] Update mriqc.sbatch fix misspelling in comment for codespell --- docs/source/resources/mriqc.sbatch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/resources/mriqc.sbatch b/docs/source/resources/mriqc.sbatch index 9327b00d..4a8ad105 100644 --- a/docs/source/resources/mriqc.sbatch +++ b/docs/source/resources/mriqc.sbatch @@ -1,7 +1,7 @@ #!/bin/bash #NOTE: These should work with Slurm HPC systems, - # but these specific paramters have only been tested on + # but these specific parameters have only been tested on # Stanford's Sherlock. Some parameters may need to be # adjusted for other HPCs, specifically --partition. From 991c38558e0e0c040c8383b1bf22de2ff366f6b2 Mon Sep 17 00:00:00 2001 From: McKenzie Paige Hagen <35019015+mckenziephagen@users.noreply.github.com> Date: Wed, 18 Sep 2024 13:47:34 -0700 Subject: [PATCH 2/2] Apply suggestions from code review Co-authored-by: Oscar Esteban --- docs/source/resources/mriqc.sbatch | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/docs/source/resources/mriqc.sbatch b/docs/source/resources/mriqc.sbatch index 4a8ad105..88beccc3 100644 --- a/docs/source/resources/mriqc.sbatch +++ b/docs/source/resources/mriqc.sbatch @@ -31,10 +31,10 @@ unset PYTHONPATH MRIQC_VERSION="24.0.0" #TODO: update if using a different version -BIDS_DIR="ds002785" #TODO: replace with path to your dataset +BIDS_DIR="${STUDY}/ds002785" # TODO: replace with path to your dataset OUTPUT_DIR="${BIDS_DIR}/derivatives/mriqc-${MRIQC_VERSION}" -SINGULARITY_CMD="singularity run -e mriqc-${MRIQC_VERSION}.simg" +SINGULARITY_CMD="apptainer run -e mriqc_${MRIQC_VERSION}.sif" #NOTE: The first clause in this line selects a row in participants.tsv # using the system generated array index variable SLURM_ARRAY_TASK_ID. @@ -49,8 +49,9 @@ echo Subject $subject cmd="${SINGULARITY_CMD} ${BIDS_DIR} ${OUTPUT_DIR} participant \ --participant-label $subject \ -w $PWD/work/ \ - --omp-nthreads 8 --mem 10 \ - --verbose-reports" + --omp-nthreads 10 --nprocs 12 \ # For nodes with at least 32GB RAM + --verbose-reports \ + --bids-database-dir ${BIDS_DIR}/.bids-index/" echo Running task ${SLURM_ARRAY_TASK_ID} echo Commandline: $cmd