brainage/Enigma/analysis.sh

#!/bin/sh


CAT_DIR=$1
WORK_DIR=$2

echo "data folder in ${CAT_DIR}"
echo "working directory is ${WORK_DIR}"

chmod -R 777 ${WORK_DIR}

cd ${WORK_DIR}
touch ${WORK_DIR}/subjs_p1.txt
touch ${WORK_DIR}/subjs_p2.txt
touch ${WORK_DIR}/affines.txt

for subject in $(find $CAT_DIR/ -maxdepth 5 -mindepth 1 -name "p1*T1w.nii" -printf '%P\n'); do 

        p1_path=${CAT_DIR}/$(dirname $subject)
        echo "subject ${p1_path}"
        # gunzip -d --force ${p1_path}/p1*T1w.nii.gz
        # gunzip -d --force ${p1_path}/p2*T1w.nii.gz
        if [ "$?" -ne 0 ]; then
            echo "${subject} failed to copy T1 in node tmp \n"
        fi
        echo \'${p1_path}/$(find ${p1_path}/ -name "p1sub*_T1w.nii" -printf '%P\n')\' >> ${WORK_DIR}/subjs_p1.txt
        echo \'${p1_path}/$(find ${p1_path}/ -name "p2sub*_T1w.nii" -printf '%P\n')\' >> ${WORK_DIR}/subjs_p2.txt
        echo \'${p1_path}/$(find ${p1_path}/ -name "t_*T1w_affine_reorient.mat" -printf '%P\n')\' >> ${WORK_DIR}/affines.txt
done

echo "creating batch files"
#make .m file 
touch ${WORK_DIR}/main_batch.txt
echo -n "for i=1:1:size(subjs) 
    clear matlabbatch
    matlabbatch{1}.spm.util.reorient.prefix = 'r_';
    matlabbatch{2}.spm.spatial.smooth.data(1) = cfg_dep('Reorient Images: Reoriented Images', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
    matlabbatch{2}.spm.spatial.smooth.fwhm = [4 4 4];
    matlabbatch{2}.spm.spatial.smooth.dtype = 0;
    matlabbatch{2}.spm.spatial.smooth.im = 0;
    matlabbatch{2}.spm.spatial.smooth.prefix = 's4';
    matlabbatch{3}.spm.spatial.coreg.write.ref = {'/extras/mask_8mm_binarized.nii,1'};
    matlabbatch{3}.spm.spatial.coreg.write.source(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
    matlabbatch{3}.spm.spatial.coreg.write.roptions.interp = 1;
    matlabbatch{3}.spm.spatial.coreg.write.roptions.wrap = [0 0 0];
    matlabbatch{3}.spm.spatial.coreg.write.roptions.mask = 0;
    matlabbatch{3}.spm.spatial.coreg.write.roptions.prefix = 'r8';
    matlabbatch{4}.spm.spatial.coreg.write.ref = {'/extras/mask_4mm_binarized.nii,1'};
    matlabbatch{4}.spm.spatial.coreg.write.source(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
    matlabbatch{4}.spm.spatial.coreg.write.roptions.interp = 1;
    matlabbatch{4}.spm.spatial.coreg.write.roptions.wrap = [0 0 0];
    matlabbatch{4}.spm.spatial.coreg.write.roptions.mask = 0;
    matlabbatch{4}.spm.spatial.coreg.write.roptions.prefix = 'r4';
    matlabbatch{5}.spm.spatial.smooth.data(1) = cfg_dep('Reorient Images: Reoriented Images', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
    matlabbatch{5}.spm.spatial.smooth.fwhm = [8 8 8];
    matlabbatch{5}.spm.spatial.smooth.dtype = 0;
    matlabbatch{5}.spm.spatial.smooth.im = 0;
    matlabbatch{5}.spm.spatial.smooth.prefix = 's8';
    matlabbatch{6}.spm.spatial.coreg.write.ref = {'/extras/mask_8mm_binarized.nii,1'};
    matlabbatch{6}.spm.spatial.coreg.write.source(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
    matlabbatch{6}.spm.spatial.coreg.write.roptions.interp = 1;
    matlabbatch{6}.spm.spatial.coreg.write.roptions.wrap = [0 0 0];
    matlabbatch{6}.spm.spatial.coreg.write.roptions.mask = 0;
    matlabbatch{6}.spm.spatial.coreg.write.roptions.prefix = 'r8';
    matlabbatch{7}.spm.spatial.coreg.write.ref = {'/extras/mask_4mm_binarized.nii,1'};
    matlabbatch{7}.spm.spatial.coreg.write.source(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
    matlabbatch{7}.spm.spatial.coreg.write.roptions.interp = 1;
    matlabbatch{7}.spm.spatial.coreg.write.roptions.wrap = [0 0 0];
    matlabbatch{7}.spm.spatial.coreg.write.roptions.mask = 0;
    matlabbatch{7}.spm.spatial.coreg.write.roptions.prefix = 'r4';

    matlabbatch{1}.spm.util.reorient.srcfiles = subjs(i);
    matlabbatch{1}.spm.util.reorient.transform.transF = affines(i);
    spm_jobman('run', matlabbatch);
end" >> ${WORK_DIR}/main_batch.txt

touch ${WORK_DIR}/p1_proc_batch.m
echo -n 'subjs={' >> ${WORK_DIR}/p1_proc_batch.m
cat ${WORK_DIR}/subjs_p1.txt >> ${WORK_DIR}/p1_proc_batch.m
echo '};' >> ${WORK_DIR}/p1_proc_batch.m
echo -n 'affines={' >> ${WORK_DIR}/p1_proc_batch.m
cat ${WORK_DIR}/affines.txt >> ${WORK_DIR}/p1_proc_batch.m
echo '};' >> ${WORK_DIR}/p1_proc_batch.m

echo "writing from ${WORK_DIR}/main_batch.txt to ${WORK_DIR}/p1_proc_batch.m"

cat ${WORK_DIR}/main_batch.txt >> ${WORK_DIR}/p1_proc_batch.m

touch ${WORK_DIR}/p2_proc_batch.m
echo -n 'subjs={' >> ${WORK_DIR}/p2_proc_batch.m
cat ${WORK_DIR}/subjs_p2.txt >> ${WORK_DIR}/p2_proc_batch.m
echo '}' >> ${WORK_DIR}/p2_proc_batch.m
echo -n 'affines={' >> ${WORK_DIR}/p2_proc_batch.m
cat ${WORK_DIR}/affines.txt >> ${WORK_DIR}/p2_proc_batch.m
echo '};' >> ${WORK_DIR}/p2_proc_batch.m

echo "writing from ${WORK_DIR}/main_batch.txt to ${WORK_DIR}/p2_proc_batch.m"
cat ${WORK_DIR}/main_batch.txt >> ${WORK_DIR}/p2_proc_batch.m

# run spm-octave
chmod 777 ${WORK_DIR}*

spm12 batch ${WORK_DIR}/p1_proc_batch.m
spm12 batch ${WORK_DIR}/p2_proc_batch.m

echo "finished resampling and smoothing"
echo "starting features extraction"

python /codes/save_feat.py ${CAT_DIR}

echo "features are saved in subject's folder"

python /codes/predict_age_stacking.py ${CAT_DIR}

echo "age prediction is saved in subject's folder"