submitting mindboggle per subject

submit_mindboggle.sh

submit_mindboggle.sh
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#!/bin/bash

base={{FULL PATH TO DATA}}

# first go to data directory, grab all subjects,
# and assign to an array
pushd $base
subjs=($(ls sub-* -d -1)) # this is set up for BIDS, but you can alter the search pattern
popd

# take the length of the array
# this will be useful for indexing later
len=$(expr ${#subjs[@]} - 1) # len - 1

echo Spawning ${#subjs[@]} sub-jobs.

# this submits a SLURM job array with same size as # of subjects
sbatch --array=0-$len ss_mindboggle.sh $base ${subjs[@]}

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ss_mindboggle.sh
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#!/bin/bash
#SBATCH --time=2-00:00:00
#SBATCH --mem=30GB
#SBATCH --cpus-per-task=8
#SBATCH -J mindboggle


base=$1
args=($@)
subjs=(${args[@]:1})


# index slurm array to grab subject
subject=${subjs[${SLURM_ARRAY_TASK_ID}]}

echo Submitted job for: ${subject}

IMG={PATH TO CONTAINER}

# assign individual working directory per subject
scratch=/om/scratch/Wed/mathias/singwork/${subject}
if [ ! -d $scratch ]; then 
  mkdir -p ${scratch}/jovyan
fi

if [ ! -d ${base}/derivatives ]; then
  mkdir -p ${base}/derivatives
fi

# preventive
unset DISPLAY

# an optional step that makes this flexible across BIDS datasets with and without sessions
fullt1path=$(ls {base}/${subject}/*/anat/${subject}*T1w.nii.gz)
t1path=${fullt1path##*${base}}

# save the command to as a string to output in job log
cmd='singularity run -B '${scratch}':/workdir -B '${base}':/data $IMG /data/'${t1path}' --id '$subject' --plugin MultiProc --out /data/derivatives/mindboggle --working /workdir'

echo $'Command :\n'${cmd}

# run the command
${cmd}