level2.sh

#!/bin/bash
base_dir=$1
subj=$2
task=$3
if [[ "$subj" != "sub-"* ]]; then
    subj=sub-${subj}
fi

result_dir=${base_dir}/${subj}/MNINonLinear/Results
cd $result_dir
runs=`ls -d *task-${task}_run-*`
runs=($runs)
n_contrasts=`ls ${result_dir}/${runs[0]}/level1.feat/stats/cope*.dtseries.nii|wc -l`

out_dir=${result_dir}/level2_${task}
rm -rf $out_dir
mkdir -p ${out_dir}/tmp
cd ${out_dir}/tmp

# make fake nifti
for run in "${runs[@]}"; do
echo $run
    for f in ${result_dir}/${run}/level1.feat/stats/*.dtseries.nii; do
        name=`basename $f`
        wb_command -cifti-convert -to-nifti $f ${run}_${name%.dtseries.nii}.nii.gz
        CIFTItemplate=$f
    done
done

# mask
for run in "${runs[@]}"; do
    f=${result_dir}/${run}/level1.feat/stats/dof
    dof=`cat $f`
    base=`dirname $f`"/.."
    fslmaths ${run}_varcope1 -bin -mul $dof ${run}_dofmask
    echo "1" >> ${out_dir}/design.txt
    echo "1" >> ${out_dir}/group.txt
done

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

#merge
i=1
while [ "$i" -le "$n_contrasts" ]; do
    fslmerge -t ${out_dir}/tmp/copes${i} *_cope${i}.nii.gz
    fslmerge -t ${out_dir}/tmp/varcopes${i} *_varcope${i}.nii.gz
    i=$(($i+1))
done

#FLAME
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

i=1
while [ "$i" -le "$n_contrasts" ]; do
    flameo --cope=${out_dir}/tmp/copes${i} \
        --vc=${out_dir}/tmp/varcopes${i} \
        --dvc=${out_dir}/tmp/dof \
        --mask=${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

for f in ${out_dir}/*.nii.gz ${out_dir}/cope*.feat/*.nii.gz; do
    wb_command -cifti-convert -from-nifti $f $CIFTItemplate ${f%.nii.gz}.dtseries.nii -reset-timepoints 1 1
done

rm -rf ${out_dir}/tmp