brainage/Enigma/run_ENIGMA_stacking.sh

#!/usr/bin/env bash
# v 1.0
DEBUG=1
# sub_file=/data/project/brainage_underrepresented/data/ds004107/sub-mind010/ses-01/anat/sub-mind010_ses-01_T1w.nii.gz
sub_path=$1
# check that this is a file
if [ -e "$sub_path" ] || [ -L "$sub_path" ]; then
    echo "Input file exists or is a symbolic link."
else
    echo "Input file does not exist, exiting."
    exit 1
fi
# dir_sub
dir_path=$(dirname "${sub_path}")
# sub_file=sub-mind010_ses-01_T1w.nii.gz (or .nii, or .mgz)
sub_file=$(basename "${sub_path}")
# sub_name=sub-mind010_ses-01_T1w
sub_name="${sub_file%%.*}"

# out_dir=derivatives/brainageR/sub-01490270a/ses-BLT11
out_dir=$2

# Container path
container_path=$3

# Save or no the intermidiate files
save=$4

# Raw file ?
raw=$5

if [ $DEBUG -eq 1 ]; then
    echo "sub_file = $sub_path"
    echo "dir_path = $dir_path"
    echo "sub_file = $sub_file"
    echo "sub_name = $sub_name"
    echo "out_dir = $out_dir"
    echo "save = $save"
    echo "raw = $raw"
fi

# create result folder and move the results in there
if [ -e "$out_dir/${sub_name}_brainageR.csv" ]; then
    echo "output file exists, exiting"
    exit 
else   
    mkdir -p $out_dir
fi

cd "${dir_path}"

datalad get "${sub_file}"


# define working dir, create a 'data' folder in it and copy the subject in.
work_dir=$(mktemp -d)
mkdir ${work_dir}/data


cp "${sub_path}" "${work_dir}/data"
datalad drop "${sub_path}"

cd ${work_dir}

# unzip as SPM/CAT work with .nii files. Remove the nii.gz file and rename sub
# gunzip only if gz file and then delete .gz file
if [[ "$sub_file" == *.gz ]]; then
    echo "The file is a .gz file."
    gunzip data/${sub_file}
    rm -f data/${sub_file}
    sub_file=${sub_file%".gz"}
else
    echo "The file is not a .gz file."
fi

# make sure permissions are ok
chmod +rwx ${work_dir}/data/$sub_file

# run singularity with brainageR code
# ----------------------------------------------------------
echo "Running the container"
#singularity exec /data/project/BrainAge4AD/tools/brainageR_dockerfile/brainageR2.1.sif brainageR -f ${work_dir}/data/${sub_file} -o ${sub_name}_brain_predicted.age.csv

if [ ${raw} -ne 0 ]; then
    singularity run -B ${work_dir}/data,$(pwd) --cleanenv ${container_path} -b /code/cat_standalone_segment_enigma.m ${sub_path}
fi
singularity run --fakeroot -B /data/project/BrainAge4AD/tools/brainage_enigma_container/CAT_stacking_container,${work_dir} ${simg_pred} ${dir_path} ${work_dir}


# Check the exit status of the previous command
if [ $? -ne 0 ]; then
    echo "Singularity container failed, exiting." >&2
    exit 1
fi
# ----------------------------------------------------------

# Moving the prediction into the output dir
mv $work_dir/${sub_name}_brain_predicted.age.csv $out_dir/${sub_name}_brainageR.csv
echo "Prediction file sub${sub_name} saved in $out_dir"

# If user wants to save intermidiate files, moving everything into output dir
if [ $save == "yes" ]; then
    mkdir -p $out_dir/${sub_name}_brainageR
    mv -r $work_dir/* $out_dir/${sub_name}_brainageR/
    echo "All files of ${sub_name} saved in $out_dir/${sub_name}_brainageR"
fi

echo "Cleaning tmp files"
rm -rf $work_dir

exit