convertOnsetTimes_ToneCounting.sh

#!/bin/bash

#Check whether the file subjList.txt exists; if not, create it
if [ ! -f subjList.txt ]; then
        ls -d sub-?? > subjList.txt
fi

#Loop over all subjects and format timing files into FSL format
for subj in `cat subjList.txt` ; do
        cd $subj/func #Navigate to the subject's func directory, which contains the timing files

        #Extract the onset times for the incongruent and congruent trials for each run. NOTE: This script only extracts the trials in which the subject made a correct response. Accuracy is nearly 100% for all subjects, but as an exercise the student can modify this to extract the incorrect trials as well.
        cat ${subj}_task-tonecounting_events.tsv | awk '{if (NR!=1 && $5=="") {print $1, $2, "1"}}' > toneCount_run1.txt
        cat ${subj}_task-tonecounting_events.tsv | awk '{if ($5=="probe") {print $1, $2, "1"}}' > toneProbe_run1.txt

        cd ../..
done