make_FSL_Timings.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-flanker_run-1_events.tsv | awk '{if ($3=="incongruent_correct") {print $1, $2, "1"}}' > incongruent_run1.txt
        cat ${subj}_task-flanker_run-1_events.tsv | awk '{if ($3=="congruent_correct") {print $1, $2, "1"}}' > congruent_run1.txt

        cat ${subj}_task-flanker_run-2_events.tsv | awk '{if ($3=="incongruent_correct") {print $1, $2, "1"}}' > incongruent_run2.txt
        cat ${subj}_task-flanker_run-2_events.tsv | awk '{if ($3=="congruent_correct") {print $1, $2, "1"}}' > congruent_run2.txt
        
        cd ../..
done