Created
April 1, 2020 16:39
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#!/bin/bash | |
# | |
#SBATCH -J fmriprep | |
#SBATCH --time=48:00:00 | |
#SBATCH -n 1 | |
#SBATCH --cpus-per-task=16 | |
#SBATCH --mem-per-cpu=8G | |
#SBATCH -p HPC # Queue names you can submit to | |
# Outputs ---------------------------------- | |
#SBATCH -o log/%A-%a.out | |
#SBATCH -e log/%A-%a.err | |
#SBATCH --mail-user=%u@domain.tld | |
#SBATCH --mail-type=ALL | |
# ------------------------------------------ | |
# Specify directories and names, change these according to the version of fmriprep | |
BIDS_DIR="$STUDY/rawdata" | |
DERIVS_DIR="$STUDY/derivatives/fmriprep-1.5.2" | |
IMAGE_NAME="poldracklab_fmriprep_1.5.2-2019-12-02-6afc1e0e96cd.simg" | |
IMAGE_DIR="$STUDY/code/singularity" | |
# Prepare some writeable bind-mount points, these are local to prevent network traffic issues | |
TEMPLATEFLOW_HOST_HOME=/tmp/templateflow-$(whoami) | |
FMRIPREP_HOST_CACHE=/tmp/fmriprep-$(whoami) | |
mkdir -p ${TEMPLATEFLOW_HOST_HOME} | |
mkdir -p ${FMRIPREP_HOST_CACHE} | |
# Make derivatives folder | |
mkdir -p ${DERIVS_DIR} | |
# Make variable to represent freesurfer license (download from the freesurfer website) | |
export SINGULARITYENV_FS_LICENSE=$STUDY/code/singularity/license.txt | |
# Make variable for the templateflow bind-mount point inside the container | |
export SINGULARITYENV_TEMPLATEFLOW_HOME="/templateflow" | |
#Specify the singularity command which sets up the environment, binds the $STUDY path to the bind mount point inside the container, and specifies the singularity image | |
SINGULARITY_CMD="singularity run --cleanenv -B $STUDY:/projectFolder -B ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME} -B $L_SCRATCH:/work $IMAGE_DIR/$IMAGE_NAME" | |
# Parse the participants.tsv file and extract one subject ID from the line corresponding to this SLURM task. | |
subject=$( sed -n -E "$((${SLURM_ARRAY_TASK_ID} + 1))s/sub-(\S*)\>.*/\1/gp" ${BIDS_DIR}/participants.tsv ) | |
# Compose the command line | |
cmd="${SINGULARITY_CMD} /projectFolder/rawdata /projectFolder/derivatives/fmriprep-1.5.2_tempflow-davidm participant --participant-label $subject -w /work --output-spaces MNI152NLin2009cAsym:res-2 anat fsnative fsaverage5 -vv --no-submm-recon --fs-license-file $SINGULARITYENV_FS_LICENSE --skip_bids_validation" | |
# Setup done, run the command | |
echo Running task ${SLURM_ARRAY_TASK_ID} | |
echo Commandline: $cmd | |
eval $cmd | |
exitcode=$? | |
# Output results to a table | |
echo "sub-$subject ${SLURM_ARRAY_TASK_ID} $exitcode" \ | |
>> ${SLURM_JOB_NAME}.${SLURM_ARRAY_JOB_ID}.tsv | |
echo Finished tasks ${SLURM_ARRAY_TASK_ID} with exit code $exitcode | |
exit $exitcode |
First, install the developmental version of templateflow:
[...]
Let me know if that helps.
Yes! We're good! We'll keep an eye on the releases, I'm guessing once fMRIPrep includes TF >= 0.6.0rc2 we can skip this step?
Thanks a lot for your help!
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@FidgetSpinneur this problem has been showing its face more frequently, so there have been some changes in developmental versions of templateflow to combat this.
First, install the developmental version of templateflow:
this should install version
0.6.0rc2
at the moment.Next, set your templateflow home to the temporary folder, and ensure you are using the S3 bucket:
Then, you can run the following command to force the skeleton to update:
Finally, you can fetch the necessary templates:
Let me know if that helps.