1 Unzip MRI images downloaded using the UKB tools

The .lis files were created by ukbfetch at the end of each dowload. They contain a single column with the list of MRI images downloaded.

for batch in {1..5}
do
${bind}/qsubshcom " echo \${TASK_ID}.\$(sed -n \"\${TASK_ID}{p;q}\" "${medici}"/T1/raw/batch"${batch}"/T1_fetch_batch"${batch}".lis) |;
file=\$(sed -n \"\${TASK_ID}{p;q}\" "${medici}"/T1/raw/batch"${batch}"/T1_fetch_batch"${batch}".lis) |;
ID=\${file:0:7} |;
echo \${file} |;
echo \${ID} |;
mkdir -p "${wd}"/FS/batch"${batch}" |;
mkdir -p "${wd}"/T1/unzip/batch"${batch}"/\${ID}/ |;
unzip -n "${medici}"/T1/raw/batch"${batch}"/\${ID}_20252_2_0.zip -d "${wd}"/T1/unzip/batch"${batch}"/\${ID}/ |;
for i in `seq 1 "${batch}"` |;
    do |;
        if [ -e "${medici}"/T2/raw/batch\${i}/\${ID}_20253_2_0.zip ] |;
        then |;
        echo "${medici}"/T2/raw/batch\${i}/\${ID}_20253_2_0.zip |;
        mkdir -p "${wd}"/T2/unzip/batch"${batch}"/\${ID}/ |;
                unzip -n "${medici}"/T2/raw/batch\${i}/\${ID}_20253_2_0.zip -d "${wd}"/T2/unzip/batch"${batch}"/\${ID}/  |;
                fi |;
    done    " 1 4G Unzip_batch_${batch} 48:00:00 "-array=1-500 -acct=UQ-IMB-CNSG" 
done

2 Processing of T1 and T2 images

• FreeSurfer 6.0 recon-all processing
  T1w and T2 FLAIR are processed together if both are available, otherwise T1w are processed by themselves.

• .mgh surface files are then converted into .asc readable text files

• ENIGMA-shape processing is performed to extract subcortical structure

• Save all useful files in the ENIGMAshapeResults and FSresults folders

If space or number of files is a limitation, you can delete all intermediate FreeSurfer files at the end of the processing by adding the extra command: ‘rm -r “${wd}"/FS/batch"${batch}”/${ID}’
This leaves you with the contents of FS/ENIGMAshapeResults and FS/FSresults only, which contain everything you need for the analyses.

for batch in {1..5}
do
${bind}/qsubshcom " echo \${TASK_ID}.\$(sed -n \"\${TASK_ID}{p;q}\" "${medici}"/T1/raw/batch"${batch}"/T1_fetch_batch"${batch}".lis) |;
file=\$(sed -n \"\${TASK_ID}{p;q}\" "${medici}"/T1/raw/batch"${batch}"/T1_fetch_batch"${batch}".lis) |;
ID=\${file:0:7} |;
echo \${file} |;
echo \${ID} |;
mkdir -p "${wd}"/FS/batch"${batch}" |;
mkdir -p "${wd}"/FS/FSresults/batch"${batch}"/\${ID}/ |;
mkdir -p "${wd}"/FS/ENIGMAshapeResults/batch"${batch}"/\${ID}/ |;
SUBJECTS_DIR=\"/working/directory/FS/batch"${batch}"/\" |;
if [ -e "${wd}"/T2/unzip/batch"${batch}"/\${ID}/T2_FLAIR/T2_FLAIR_unbiased_brain.nii.gz ] |;
then |;
"${fsdir}"/bin/recon-all -subject \${ID} -i "${wd}"/T1/unzip/batch"${batch}"/\${ID}/T1/T1_orig_defaced.nii.gz -T2 "${wd}"/T2/unzip/batch"${batch}"/\${ID}/T2_FLAIR/T2_FLAIR_orig_defaced.nii.gz -T2pial -all -qcache  |;
else |;
"${fsdir}"/bin/recon-all -subject \${ID} -i "${wd}"/T1/unzip/batch"${batch}"/\${ID}/T1/T1_orig_defaced.nii.gz  -all -qcache   |;
fi |;
"${fsdir}"/bin/mris_convert -c "${wd}"/FS/batch"${batch}"/\${ID}/surf/lh.area.fwhm0.fsaverage.mgh "${fsdir}"/subjects/fsaverage/surf/lh.orig "${wd}"/FS/FSresults/batch"${batch}"/\${ID}/lh.area.fwhm0.fsaverage.asc |;
"${fsdir}"/bin/mris_convert -c "${wd}"/FS/batch"${batch}"/\${ID}/surf/rh.area.fwhm0.fsaverage.mgh "${fsdir}"/subjects/fsaverage/surf/rh.orig "${wd}"/FS/FSresults/batch"${batch}"/\${ID}/rh.area.fwhm0.fsaverage.asc |;
"${fsdir}"/bin/mris_convert -c "${wd}"/FS/batch"${batch}"/\${ID}/surf/lh.thickness.fwhm0.fsaverage.mgh "${fsdir}"/subjects/fsaverage/surf/lh.orig "${wd}"/FS/FSresults/batch"${batch}"/\${ID}/lh.thickness.fwhm0.fsaverage.asc |;
"${fsdir}"/bin/mris_convert -c "${wd}"/FS/batch"${batch}"/\${ID}/surf/rh.thickness.fwhm0.fsaverage.mgh "${fsdir}"/subjects/fsaverage/surf/rh.orig "${wd}"/FS/FSresults/batch"${batch}"/\${ID}/rh.thickness.fwhm0.fsaverage.asc |;
perl "${bind}"/ENIGMA_shape/MedialDemonsShared/bin/Medial_Demons_shared.pl "${wd}"/FS/batch"${batch}"/\${ID}/mri/aseg.mgz 10 11 12 13 17 18 26 49 50 51 52 53 54 58 "${wd}"/FS/batch"${batch}"/\${ID}/ENIGMA_shape/ "${bind}"/ENIGMA_shape/MedialDemonsShared "${fsdir}"/bin |;
rsync -r "${wd}"/FS/batch"${batch}"/\${ID}/ENIGMA_shape/* "${wd}"/FS/ENIGMAshapeResults/batch"${batch}"/\${ID}/ |; 
rsync -r "${wd}"/FS/batch"${batch}"/\${ID}/stats/* "${wd}"/FS/FSresults/batch"${batch}"/\${ID}/ |;
rsync -r "${wd}"/FS/batch"${batch}"/\${ID}/surf/*.mgh "${wd}"/FS/FSresults/batch"${batch}"/\${ID}/ |;
" 1 4G MRI_processing_batch${batch} 48:00:00 "-array=1-500 -acct=UQ-IMB-CNSG" 
done

3 Check completion of image processing

Creates files IDs_rerun_batch$batch.txt that contain IDs of participants for which processing did not complete.
You may want to re-run processing for those individuals or investigate.

for batch in {1..5}
do 
touch $wd/FS/IDs_rerun_batch$batch.txt

for file in $(awk -F" " 'NR>1 {print $1}' ${medici}/T1/raw/batch${batch}/T1_fetch_batch${batch}.lis)
do
ID=${file:0:7}
nb=$(ls ${wd}/FS/FSresults/batch${batch}/${ID}/*.asc | wc -l)
if [ ${nb} -lt 4 ]
then
if [ ! -d ${wd}/T1/unzip/batch${batch}/$ID/T1/unusable/ ]
then
echo "Processing fail investigate"
echo ${ID} 
echo ${nb}
echo ${ID} >> $wd/FS/IDs_rerun_batch$batch.txt
fi
fi
done