level2_volume.sh

#!/bin/bash
# run second level across runs
result_dir=$1
subj=$2
task=$3
session=''
if [ "$#" -lt 3 ]; then
    echo "Usage: level2_volume.sh RESULT_DIR SUBJECT TASK [SESSION]"
fi

if [ "$#" -eq 4 ]; then
    session="ses-${4}_"
fi

out_dir=${result_dir}/sub-${subj}/sub-${subj}_${session}task-${task}_level2
rm -rf $out_dir
runs=`ls -d ${result_dir}/sub-${subj}/sub-${subj}_${session}task-${task}_run-*_bold`
runs=($runs)
mkdir -p ${out_dir}/tmp

# mask
for i in "${!runs[@]}"; do
    f=${runs[$i]}/stats/dof
    dof=`cat $f`
    base=`dirname $f`"/.."
    fslmaths ${runs[$i]}/stats/varcope1 -bin -mul $dof ${out_dir}/tmp/${i}_dofmask
    echo "1" >> ${out_dir}/design.txt
    echo "1" >> ${out_dir}/group.txt
done

fslmerge -t  ${out_dir}/dof ${out_dir}/tmp/*_dofmask.nii.gz
fslmaths ${out_dir}/dof -Tmin -bin ${out_dir}/mask

#merge
n_contrasts=`ls ${runs[0]}/stats/cope*|wc -l`
i=1
while [ "$i" -le "$n_contrasts" ]; do
    fslmerge -t ${out_dir}/tmp/copes${i} ${result_dir}/sub-${subj}/sub-${subj}_${session}task-${task}_run-*_bold/stats/cope${i}.nii.gz
    fslmerge -t ${out_dir}/tmp/varcopes${i} ${result_dir}/sub-${subj}/sub-${subj}_${session}task-${task}_run-*_bold/stats/varcope${i}.nii.gz
    i=$(($i+1))
done

#design
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=${out_dir}/dof \
        --mask=${out_dir}/mask \
        --ld=${out_dir}/cope${i}.feat \
        --dm=${out_dir}/design.mat \
        --cs=${out_dir}/design.grp \
        --tc=${out_dir}/design.con \
        --runmode=fe
    i=$(($i+1))
done

# rm -rf ${out_dir}/tmp