level3_randomise.sh

#!/bin/bash
# run second level across runs
result_dir=$1
task=$2
nperm=$3 #fe, ols, or flame1

out_dir=${result_dir}/task-${task}_level3_randomise
rm -r $out_dir
inputs=`ls -d ${result_dir}/sub-*/sub-*_task-${task}_level2`
inputs=($inputs)
mkdir -p ${out_dir}/tmp

# merge files
n_contrasts=`ls -d ${inputs[0]}/cope*.feat|wc -l`
i=1
while [ "$i" -le "$n_contrasts" ]; do
    fslmerge -t ${out_dir}/tmp/copes${i} ${result_dir}/sub-*/sub-*_task-${task}_level2/cope${i}.feat/cope1.nii.gz
    fslmerge -t ${out_dir}/tmp/varcopes${i} ${result_dir}/sub-*/sub-*_task-${task}_level2/cope${i}.feat/varcope1.nii.gz
    fslmerge -t ${out_dir}/tmp/tdof${i} ${result_dir}/sub-*/sub-*_task-${task}_level2/cope${i}.feat/tdof_t1.nii.gz
    fslmaths ${out_dir}/tmp/tdof${i} -Tmin -bin ${out_dir}/tmp/mask${i}
    i=$(($i+1))
done

# resample background
flirt -in ${FSLDIR}/data/standard/avg152T1_brain.nii.gz \
    -applyxfm -init ${FSLDIR}/etc/flirtsch/ident.mat \
    -out ${out_dir}/background -paddingsize 0.0 -interp trilinear \
    -ref ${out_dir}/tmp/mask1

#design
for i in "${!inputs[@]}"; do
    echo "1" >> ${out_dir}/design.txt
    echo "1" >> ${out_dir}/group.txt
done
echo "1" > ${out_dir}/contrast.txt
echo "-1" >> ${out_dir}/contrast.txt

Text2Vest ${out_dir}/design.txt ${out_dir}/design.mat
Text2Vest ${out_dir}/contrast.txt ${out_dir}/design.con
Text2Vest ${out_dir}/group.txt ${out_dir}/design.grp

# run randomise
# variance smoothing
v_option=''
if [[ "${#inputs[@]}" -le 20 ]]; then
    v_option='-v 5'
fi
i=1
while [ "$i" -le "$n_contrasts" ]; do
    mkdir ${out_dir}/cope${i}
    randomise -i ${out_dir}/tmp/copes${i} \
    -o ${out_dir}/cope${i}/ \
    -d ${out_dir}/design.mat \
    -t ${out_dir}/design.con \
    -m ${out_dir}/tmp/mask${i} \
    -n $nperm \
    -T -R --uncorrp --seed=1234 $v_option
    i=$(($i+1))
done

#cluster
i=1
while [ "$i" -le "$n_contrasts" ]; do
    cd ${out_dir}/cope${i}
    for dir in 1 2; do
        easythresh _tfce_corrp_tstat${dir}.nii.gz .95 ../background.nii.gz cluster${dir}
        cluster -i _tfce_corrp_tstat${dir}.nii.gz -t .95 -o cluster_mask_cluster${dir} --mm > cluster_cluster${dir}.txt
    done
    i=$(($i+1))
done

rm -rf ${out_dir}/tmp