level3_flame.sh

#!/bin/bash
result_dir=$1
out_dir=$2
subjects_file=$3
task=$4

subjects=`cat $subjects_file | tr "\n" " "`
subjects=($subjects)
n_contrasts=`ls -d ${result_dir}/sub-${subjects[0]}/MNINonLinear/Results/level2_${task}/cope*.feat|wc -l`

# for every second level cope
for cope in `seq $n_contrasts`; do
    rm -r ${out_dir}/cope${cope}
    mkdir -p ${out_dir}/cope${cope}/tmp
    cd $out_dir/cope${cope}/tmp

    #merge input files
    for fname in varcope1 cope1 tdof_t1 mask; do
        cmd="fslmerge -t ${fname} "
        for s in ${subjects[@]}; do
            cmd="$cmd  ${result_dir}/sub-${s}/MNINonLinear/Results/level2_${task}/cope${cope}.feat/${fname}.nii.gz"
        done
        echo $cmd
        `$cmd`
    done

    # create mask
    fslmaths mask -Tmin -bin group_mask

    #design
    for i in "${!subjects[@]}"; do
        echo "1" >> design.txt
        echo "1" >> group.txt
    done
    echo "1" > contrast.txt
    echo "-1" >> contrast.txt
    Text2Vest design.txt design.mat
    Text2Vest contrast.txt design.con
    Text2Vest group.txt design.grp

    # estimate
    flameo --cope=cope1 \
        --vc=varcope1 \
        --dvc=tdof_t1 \
        --mask=group_mask \
        --ld=../../cope${cope}.gfeat \
        --dm=design.mat \
        --cs=design.grp \
        --tc=design.con \
        --runmode=flame1

    # CIFTI
    cd ../../cope${cope}.gfeat
    CIFTItemplate=${result_dir}/sub-${subjects[0]}/MNINonLinear/Results/level2_${task}/cope${cope}.feat/pe1.dtseries.nii
    for f in *.nii.gz; do
        wb_command -cifti-convert -from-nifti $f $CIFTItemplate ${f%.nii.gz}.dtseries.nii -reset-timepoints 1 1
    done

    # cleanup
    rm *.nii.gz
    rm -r ${out_dir}/cope${cope}
done