Commit ba772802 authored by Alex Waite's avatar Alex Waite

fmriprep: bind-mount all important dirs

This is regardless if they're automatically bound or not. It helps avoid
footguns as the user adjusts this to their needs.
parent 5f3a30bb
#!/bin/bash
# v1.2
# v1.3
CPUS='1'
RAM='8G'
......@@ -7,6 +7,7 @@ DISK='90G'
LOGS_DIR=~/htcondor-templates/fmriprep/logs
FMRIPREP='/data/project/singularity/fmriprep-20.0.5.simg'
WORK_DIR='/tmp'
BIDS_DIR='/data/project/llamas'
OUTPUT_DIR='/data/project/llamas/Derivatives'
......@@ -28,11 +29,11 @@ executable = /usr/bin/singularity
# loop over all subjects
for sub in sub-{01..36}; do
printf "arguments = run --cleanenv -B ${BIDS_DIR},/opt/freesurfer/6.0/license.txt:/opt/freesurfer/license.txt \
printf "arguments = run --cleanenv -B ${WORK_DIR},${BIDS_DIR},${OUTPUT_DIR},/opt/freesurfer/6.0/license.txt:/opt/freesurfer/license.txt \
${FMRIPREP} \
--n_cpus ${CPUS} \
--skull-strip-fixed-seed \
--work-dir /tmp \
--work-dir ${WORK_DIR} \
${BIDS_DIR} ${OUTPUT_DIR} participant \
--participant-label ${sub}\n"
printf "log = ${LOGS_DIR}/\$(Cluster).\$(Process).${sub}.log\n"
......
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