run_1stLevel_Analysis_Gambles.sh

#!/bin/bash

# Generate the subject list to make modifying this script
# to run just a subset of subjects easier.

for id in `seq -w 1 16` ; do
    subj="sub-$id"
    echo "===> Starting processing of $subj"
    echo
    cd $subj
        
        # If the brain mask doesn’t exist, create it
        if [ ! -f anat/${subj}_T1w_brain.nii.gz ]; then
            echo "Skull-stripped brain not found, creating it..."
            # Note: This fractional intensity appears to work well for most of the subjects in the
            # Flanker dataset. You may want to change it if you modify this script for your own study.
            bet2 anat/${subj}_T1w.nii.gz \
                anat/${subj}_T1w_brain.nii.gz
        fi

        # Copy the design files into the subject directory, and then
        # change “sub-01” to the current subject number
        cp ../design_run1.fsf .
        cp ../design_run2.fsf .
        cp ../design_run3.fsf .

        # Note that we are using the | character to delimit the patterns
        # instead of the usual / character because there are / characters
        # in the pattern.
        sed -i '' "s|sub-01|${subj}|g" \
            design_run1.fsf
        sed -i '' "s|sub-01|${subj}|g" \
            design_run2.fsf
        sed -i '' "s|sub-01|${subj}|g" \
            design_run3.fsf

        # Now everything is set up to run feat
        echo "===> Starting feat for run 1"
        feat design_run1.fsf
        echo "===> Starting feat for run 2"
        feat design_run2.fsf
        echo "===> Starting feat for run 3"
        feat design_run3.fsf
                echo

    # Go back to the directory containing all of the subjects, and repeat the loop
    cd ..
done

echo