CoCalc provides the best real-time collaborative environment for Jupyter Notebooks, LaTeX documents, and SageMath, scalable from individual users to large groups and classes!

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#! /bin/bash
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export SUBJECTS_DIR=/workspace
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export input_path=/workspace/data/raw
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ids=()
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for dirname in /${input_path}/*; do
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    subj_id=${dirname#/${input_path}/}  # remove "/input/sub-"
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    subj_id=${subj_id%/}  # remove trailing "/"
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    if [[ ! -d "/output/$subj_id" ]]; then
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        ids+=( "$subj_id" )
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    fi
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done
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printf 'Found ID: %s\n' "${ids[@]}" >&2
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printf '%s\n' "${ids[@]}" | parallel --jobs 10 --timeout 250% --progress recon-all -expert /workspace/data/expert.opts -s {.} -i ${input_path}/{.}/unprocessed/3T/T1w_MPR1/{.}_3T_T1w_MPR1.nii.gz -all -qcache
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