slicetimeextract

#!/bin/bash

# extracts slice timing data from bids json and writes it to
# FSL compatible file in OUTPUTDIR

usage(){
    echo "Usage: $(basename $0) INPUTFILE OUTPUTDIRECTORY"
    echo "INPUTFILE should be a BIDS functional sidecar json file"
    echo "OUTPUTDIRECTORY is where I will write your FSL-compatible slice timing"
    echo "I will write foo_bold.json to OUTPUTDIRECTORY/foo_slicetimes.txt"
    exit 1
}

[[ $# -eq 2 ]] || usage

INPUTFILE=$1
OUTPUTDIR=$2
OUTNAME=$(basename $INPUTFILE)
OUTNAME=${OUTNAME/%_bold.json/_slicetimes.txt}
/usr/bin/jq .SliceTiming[] < $1 > $OUTPUTDIR/$OUTNAME