renameToBIDSAnySession is a bash script designed to create symlinks for neuroimaging data files in a BIDS (Brain Imaging Data Structure) format. The script processes structural, diffusion, and rfMRI files, creating the appropriate directory structure and symlinks.

renameToBIDSAnySession.sh

#!/bin/bash

# Initialize variables
input_dir="/path/to/input/directory"
bids_root="/path/to/BIDS/rawdata/"
log_file="logs/$(date +%Y%m%d_%H%M%S)_renameToBIDSAnySession.log"
cases=""
case_list=""

# Function to display help message
usage() {
    echo "Usage: $0 -i input_dir -o bids_root [-l log_file] [-c cases] [-f case_list]"
    echo "  -i input_dir   : Input directory (e.g., '/path/to/Protocol/*')"
    echo "  -o bids_root   : BIDS root directory"
    echo "  -l log_file    : Log file (optional)"
    echo "  -c cases       : Specific cases to process (e.g., '5017_MR1 5018_MR2') (optional)"
    echo "  -f case_list   : Path to a file containing a list of cases to process (optional)"
    exit 1
}

# Parse command line arguments
while getopts "i:o:l:c:f:h" opt; do
    case ${opt} in
        i) input_dir=${OPTARG} ;;
        o) bids_root=${OPTARG} ;;
        l) log_file=${OPTARG} ;;
        c) cases=${OPTARG} ;;
        f) case_list=${OPTARG} ;;
        h) usage ;;
        *) usage ;;
    esac
done

# Check for required arguments
if [ -z "${input_dir}" ] || [ -z "${bids_root}" ]; then
    usage
fi

# Create logs directory if it does not exist
if [ ! -d "logs" ]; then
    mkdir logs
fi

# Create log file
touch ${log_file}

# Change to BIDS root directory
cd ${bids_root} || { echo "Error: Cannot change to BIDS root directory ${bids_root}"; exit 1; }

# Function to create symlinks and handle broken links
create_symlink() {
    local from=$1
    local to=$2

    if [ -f ${from} ]; then
        ln -s ${from} ${to}
        echo "moving ${from}"
        echo "new file is $(ls ${to})"
    else
        echo "Warning: Source file ${from} does not exist. Logging to ${log_file}"
        echo "$(date +%Y-%m-%d\ %H:%M:%S) - Broken symlink: ${from} -> ${to}" >> ${log_file}
    fi

    # Check if the symlink is broken
    if [ -L ${to} ] && [ ! -e ${to} ]; then
        echo "Warning: Symlink ${to} is broken. Logging to ${log_file}"
        echo "$(date +%Y-%m-%d\ %H:%M:%S) - Broken symlink: ${to}" >> ${log_file}
    fi
}

# Function to process each case
process_case() {
    local case=$1

    echo -e '\n\n'
    echo "Processing ${case}"

    local sub_dir="sub-${case%_MR*}"
    local ses_dir="ses-${case#????_MR}"

    mkdir -p ${sub_dir}/${ses_dir}/anat
    mkdir -p ${sub_dir}/${ses_dir}/dwi
    mkdir -p ${sub_dir}/${ses_dir}/func

    # Process Structural files
    find ${input_dir}/${case}/unprocessed/3T/ -type f \( -name "*T1w*" -o -name "*T2w*" \) | while read -r from; do
        base_name=$(basename ${from})
        ext="${base_name##*.}"
        modality=$(echo ${base_name} | grep -oP '(T1w|T2w)')
        to=${sub_dir}/${ses_dir}/anat/${sub_dir}_${ses_dir}_${modality}.${ext}
        create_symlink ${from} ${to}
    done

    # Process Diffusion files
    find ${input_dir}/${case}/unprocessed/3T/Diffusion/ -type f \( -name "*.bval" -o -name "*.bvec" -o -name "*.nii.gz" -o -name "*.json" \) | while read -r from; do
        base_name=$(basename ${from})
        ext="${base_name##*.}"
        dir=$(echo ${base_name} | grep -oP '(dir\d+)')
        phase=$(echo ${base_name} | grep -oP '(AP|PA)')
        to=${sub_dir}/${ses_dir}/dwi/${sub_dir}_${ses_dir}_acq-${phase}_${dir}_dwi.${ext}
        create_symlink ${from} ${to}
    done

    # Process rfMRI files
    find ${input_dir}/${case}/unprocessed/3T/ -type f \( -name "*rfMRI*" -o -name "*REST*" \) | while read -r from; do
        base_name=$(basename ${from})
        ext="${base_name##*.}"
        run=$(echo ${base_name} | grep -oP '(REST\d+)')
        phase=$(echo ${base_name} | grep -oP '(AP|PA)')
        to=${sub_dir}/${ses_dir}/func/${sub_dir}_${ses_dir}_task-rest_acq-${phase}_run-${run#REST}_bold.${ext}
        create_symlink ${from} ${to}
    done
}

# Function to read cases from a file
read_cases_from_file() {
    local file=$1
    while IFS= read -r line; do
        cases="${cases} ${line}"
    done < ${file}
}

# Process specified cases, read cases from file, or find all cases if not specified
if [ -n "${case_list}" ]; then
    read_cases_from_file ${case_list}
fi

if [ -n "${cases}" ]; then
    # Split the case list into individual cases
    IFS=' ' read -r -a case_array <<< "${cases}"
    for case in "${case_array[@]}"; do
        process_case ${case}
    done
else
    find ${input_dir} -mindepth 1 -maxdepth 1 -type d -exec basename {} \; | while read -r case; do
        process_case ${case}
    done
fi

renameToBIDSAnySession

Overview

renameToBIDSAnySession is a bash script designed to create symlinks for neuroimaging data files in a BIDS (Brain Imaging Data Structure) format. The script processes structural, diffusion, and rfMRI files, creating the appropriate directory structure and symlinks.

Features

• Dynamically processes cases found in the input directory or specified through command-line arguments or a case list file.
• Creates appropriate BIDS-compliant directory structure and symlinks.
• Logs broken symlink attempts.

Usage

./renameToBIDSAnySession.sh -i input_dir -o bids_root [-l log_file] [-c cases] [-f case_list]

Parameters

• -i input_dir : The input directory containing the neuroimaging data (e.g., /path/to/Protocol/*).
• -o bids_root : The BIDS root directory where the symlinks will be created.
• -l log_file (optional) : The path to the log file. Defaults to logs/$(date +%Y%m%d_%H%M%S)_renameToBIDSAnySession.log.
• -c cases (optional) : Specific cases to process, provided as a quoted string with space-separated case identifiers (e.g., '5017_MR1 5018_MR2').
• -f case_list (optional) : Path to a file containing a list of cases to process, with one case per line.

Examples

Process Specific Cases

To process specific cases provided as command-line arguments:

./renameToBIDSAnySession.sh -i /rfanfs/pnl-zorro/projects/Neuroprogression/Protocol/* -o /rfanfs/pnl-zorro/projects/Neuroprogression/data_processing/BIDS2/rawdata/ -c "5005_MR1 5012_MR2 4121_MR2 5013_MR3 5013_MR2 5014_MR2 5022_MR2 5020_MR2"

Process Cases from a File

To process cases listed in a file (e.g., case_list.txt):

./renameToBIDSAnySession.sh -i /rfanfs/pnl-zorro/projects/Neuroprogression/Protocol/* -o /rfanfs/pnl-zorro/projects/Neuroprogression/data_processing/BIDS2/rawdata/ -f /path/to/case_list.txt

Process All Cases

To process all cases found in the input directory:

./renameToBIDSAnySession.sh -i /rfanfs/pnl-zorro/projects/Neuroprogression/Protocol/* -o /rfanfs/pnl-zorro/projects/Neuroprogression/data_processing/BIDS2/rawdata/

Logging

The script logs any broken symlink attempts to the specified log file. If no log file is specified, it defaults to logs/$(date +%Y%m%d_%H%M%S)_renameToBIDSAnySession.log. Ensure the logs directory exists or will be created by the script.

Script Details

Function: create_symlink

Creates a symlink from the source file to the target location. Logs any broken symlink attempts.

Function: process_case

Processes a single case, creating the appropriate directory structure and symlinks for structural, diffusion, and rfMRI files.

Function: read_cases_from_file

Reads cases from a specified file and appends them to the cases variable.

Handling Command Line Arguments

The script handles command line arguments using getopts, supporting both specific cases and case list files.

Requirements

• Bash shell
• Linux or macOS environment

License

This project is licensed under the MIT License. See the LICENSE file for details.