level3_volume.sh

#!/bin/bash
# run second level across runs
result_dir=$1
task=$2
runmode=flame1 #fe, ols, or flame1
thr=3.1 # cluster height
pthr=.05 # cluster p

out_dir=${result_dir}/task-${task}_level3
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 FLAME
i=1
while [ "$i" -le "$n_contrasts" ]; do
    flameo --cope=${out_dir}/tmp/copes${i} \
        --vc=${out_dir}/tmp/varcopes${i} \
        --dvc=${out_dir}/tmp/tdof${i} \
        --mask=${out_dir}/tmp/mask${i} \
        --ld=${out_dir}/cope${i}.gfeat \
        --dm=${out_dir}/design.mat \
        --cs=${out_dir}/design.grp \
        --tc=${out_dir}/design.con \
        --runmode=$runmode

    i=$(($i+1))
done

#cluster
i=1
while [ "$i" -le "$n_contrasts" ]; do
    cd ${out_dir}/cope${i}.gfeat
    for dir in 1 2; do
        easythresh zstat${dir} mask $thr $pthr ../background.nii.gz cluster${dir} --mm
    done
    i=$(($i+1))
done

# rm -rf ${out_dir}/tmp