#init

Create bulk file


bind="/network/lustre/iss02/ukbiobank/software" 
wd="/network/lustre/iss02/ukbiobank/unorganized/unorganized_pheno"
cd $wd
${bind}/ukbconv ukb673035.enc_ukb bulk -s20252

Extract first visits (remove imaging second wave)

blk = read.table("../ukb673035.bulk", stringsAsFactors = F)

table(blk$V2)
write.table(blk[-which(blk$V2 == "20263_3_0"), ], "../ukb673035.20263_2.bulk",
    col.names = F, row.names = F, quote = F)

#Remove unusable subjects (that I gotten through the FSL process (_20252)) #no need to do that because we will at the end remove all subjects that dont have both T1

getwd()
blk_v2 = read.table("../ukb673035.20263_2.bulk", stringsAsFactors = F)
blk <- read.table("../ukb50815.20263.bulk", stringsAsFactors = F)
unusable = read.table("../unusable_20252.csv", header = F)
usables = setdiff(blk_v2$V1, unusable$V1)
usables = setdiff(blk$V1, unusable$V1)

ukb_usable = blk_v2[blk_v2$V1 %in% usables, ]
ukb_usable = blk[blk$V1 %in% usables, ]

dim(ukb_usable)
write.table(ukb_usable, "../ukb50815_20263_usable.bulk", col.names = F,
    row.names = F, quote = F)

Create batch bulk files to parallelise the analysis and subbatches

wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"

cd $wd/Downloadfs
split -l 1000 ukb50815_20263_usable.bulk ukb50815.20263.bulk.batch --numeric-suffixes=1 

rd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant/Downloadfs" # reading directory (created above)

for batch in 43
do
# 1) Split ID list of each batch into 8 sublists
split -l$((`wc -l < ${rd}/ukb50815.20263.bulk.batch${batch}`/8)) ${rd}/ukb50815.20263.bulk.batch${batch} ${rd}/ukb50815.20263.bulk.batch${batch}_subbatch -da 1
done

Dowload UKB bulk data - FreeSurfer processing


bind="/network/lustre/iss02/ukbiobank/software" 
ukb="/network/lustre/iss02/ukbiobank/unorganized/unorganized_pheno" # UKB files
wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"

mkdir -p ${wd}/Downloadfs
cp ${wd}/ukb50815.20263.bulk ${wd}/Downloadfs/ukb50815.20263.bulk
cp ${ukb}/k53185r50815.key ${wd}/Downloadfs/k53185r50815.key

#new key 
cp ${ukb}/k53185r673035.key ${wd}/Downloadfs/k53185r673035.key


bind="/network/lustre/iss02/ukbiobank/software" 
ukb="/network/lustre/iss02/ukbiobank/unorganized/unorganized_pheno" # UKB files
wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"

cd ${wd}/Downloadfs
bind="/network/lustre/iss02/ukbiobank/software" 

for step in $(seq 42000 1 42275)   # ....
do 
${bind}/ukbfetch -bukb50815_20263_usable.bulk -ak53185r673035.key -s${step} -m1
done 


ukbfetch -bukb673035.bulk -s1 -m1000
ukbfetch -bukb673035.bulk -s1001 -m2000
ukbfetch -bukb673035.bulk -s2001 -m3000

wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"

# Check number of downloaded filesvas ya 
for batch in {14..} # ...
do
for iii in {1..3}
do
dat=$(sed -n "${iii}{p;q}" ${rd}/ukb50815.20263.bulk.batch${batch})
ID=$(echo ${dat} | cut -f 1 -d ' ' ) 
ls ${wd}/Downloadfs/*${ID}*
done 
done

Finalise FS processing and perform ENIGMA-shape analysis

#25 min environ par suj



# Set environment and run
bind="/network/lustre/iss02/ukbiobank/software" 
ukb="/network/lustre/iss02/ukbiobank/unorganized/unorganized_pheno" 
wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"
rd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant/Downloadfs" # reading directory (created above)
fsdir="/network/lustre/iss01/apps/software/noarch/freesurfer/freesurfer_6.0.0"

mkdir -p ${wd}/FSProcessing
cd ${rd}

for batch in 43
do
${bind}/qsubshcom " dat=\$(sed -n \"\${TASK_ID}{p;q}\" ${rd}/ukb50815.20263.bulk.batch${batch}) |;
ID=\$(echo \${dat} | cut -f 1 -d ' ' ) |;
field=\$(echo \${dat} | cut -f 2 -d ' ' ) |;
echo \${ID} |;
mkdir -p ${wd}/FSOUTPUT/batch${batch}/FSresults/\${ID}/ |;
mkdir -p ${wd}/FSOUTPUT/batch${batch}/ENIGMAshapeResults/\${ID}/ |;
mkdir -p ${wd}/FSProcessing/batch${batch}/\${ID}/ |;
unzip \${ID}_\${field}.zip -d ${rd}/\${ID} |;
mv ${rd}/\${ID}/FreeSurfer/* ${wd}/FSProcessing/batch${batch}/\${ID}/ |;
module load FreeSurfer |; 
SUBJECTS_DIR="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant/FSProcessing/batch${batch}" |;
"${fsdir}"/bin/recon-all -subject \${ID} -qcache |;
SUBJECTS_DIR="/network/lustre/iss01/apps/software/noarch/freesurfer/freesurfer_6.0.0/subjects" |; 

for hemi in lh rh |; do |;
for moda in area thickness |; do |;
for fwhm in 0 5 10 15 20 25 |; do |;
"${fsdir}"/bin/mris_convert -c ${wd}/FSProcessing/batch${batch}/\${ID}/surf/\${hemi}.\${moda}.fwhm\${fwhm}.fsaverage.mgh "${fsdir}"/subjects/fsaverage/surf/\${hemi}.orig ${wd}/FSOUTPUT/batch${batch}/FSresults/\${ID}/\${hemi}.\${moda}.fwhm\${fwhm}.fsaverage.asc |;
done |; 
for fsav in fsaverage3 fsaverage4 fsaverage5 fsaverage6 |; do |;
"${fsdir}"/bin/mri_surf2surf --s fsaverage --hemi \${hemi} --sval ${wd}/FSProcessing/batch${batch}/\${ID}/surf/\${hemi}.\${moda}.fwhm0.fsaverage.mgh --trgsubject \${fsav} --tval ${wd}/FSProcessing/batch${batch}/\${ID}/surf/\${hemi}.\${moda}.fwhm0.\${fsav}.mgh |;
"${fsdir}"/bin/mris_convert -c ${wd}/FSProcessing/batch${batch}/\${ID}/surf/\${hemi}.\${moda}.fwhm0.\${fsav}.mgh "${fsdir}"/subjects/\${fsav}/surf/\${hemi}.orig ${wd}/FSOUTPUT/batch${batch}/FSresults/\${ID}/\${hemi}.\${moda}.fwhm0.\${fsav}.asc |;
done |;
done |; done |;
perl "${bind}"/ENIGMA_shape/MedialDemonsShared/bin/Medial_Demons_shared.pl ${wd}/FSProcessing/batch${batch}/\${ID}/mri/aseg.mgz 10 11 12 13 17 18 26 49 50 51 52 53 54 58 ${wd}/FSProcessing/batch${batch}/\${ID}/ENIGMA_shape/ "${bind}"/ENIGMA_shape/MedialDemonsShared "${fsdir}"/bin |;
rsync -r ${wd}/FSProcessing/batch${batch}/\${ID}/ENIGMA_shape/* ${wd}/FSOUTPUT/batch${batch}/ENIGMAshapeResults/\${ID}/ |;
rsync -r ${wd}/FSProcessing/batch${batch}/\${ID}/stats/* ${wd}/FSOUTPUT/batch${batch}/FSresults/\${ID}/ |;
rm -r ${rd}/\${ID}_\${field}.zip |;
echo ${rd}/\${ID}_\${field}.zip|;
rm -r ${rd}/\${ID} |;
rm -r ${wd}/FSProcessing/batch${batch}/\${ID}|;  
" 1 4G UKB_batch${batch}_FastProcessing 4:00:00 "--partition=bigmem -array=1-272"
done


# Remove  batches, once the files have been created
wd="/working/directory"
for batch in 1
do
rm -r ${wd}/FSOUTPUT/batch${batch}/
rm -r ${wd}/FSProcessing/batch${batch}/
done

Check progression of processing


# Start interactive job - PBPpro queue
# qsub -I -l select=1:ncpus=1:mem=5GB -l walltime=05:00:00 -A UQ-IMB-CNSG
srun -p normal -N 1 -c 1 --mem=5G --time=0-03:00:00 --pty bash # SLURM

wd="/working/directory"
rd="/working/directory/Download"
fsdir="/path/to/freesurfer  
bind="/software/and/binary/directory" 
cd ${wd}


for batch in 1 2 3 4 #..
do
rm $wd/FSOUTPUT/IDs_rerun_investigateProcessing_Cortical_batch${batch}.txt
rm $wd/FSOUTPUT/IDs_rerun_investigateProcessing_Subortical_batch${batch}.txt

for iii in {1..1000}
do
dat=$(sed -n "${iii}{p;q}" ${rd}/20263.bulk.batch${batch})
ID=$(echo ${dat} | cut -f 1 -d ' ' ) 
echo ${ID}
nb=$(ls $wd/FSOUTPUT/batch${batch}/FSresults/${ID}/ | wc -l)
if [ ${nb} -lt 58 ] 
then
echo "Cortical processing failed"
echo ${nb}
echo ${dat} >> $wd/FSOUTPUT/IDs_rerun_investigateProcessing_Cortical_batch${batch}.txt
fi
nb=$(ls $wd/FSOUTPUT/batch${batch}/ENIGMAshapeResults/${ID}/ | wc -l)
if [ ${nb} -lt 56 ]
then
echo "Subortical processing failed"
echo ${nb}
echo ${dat} >> $wd/FSOUTPUT/IDs_rerun_investigateProcessing_Subcortical_batch${batch}.txt
fi
done
done

Create vertex-wise datasets

Faster version - parallelised Uses first indiv from batch 1 to get the column names



#2) Submit jobs on sublists (8x faster)
bind="/network/lustre/iss02/ukbiobank/software" 
wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"
rd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant/Downloadfs" # reading directory (created above)

for batch in 43 # ...
do
cd ${wd}/FSOUTPUT/batch${batch}/FSresults #Get the name of the first folder in the FSoutput/batch 
first=$(ls -d */ | head -1)
for hemi in lh rh
do
for moda in area thickness
do
cd ${wd}/FSProcessing
echo ${hemi}.${moda}
${bind}/qsubshcom " echo \"vertexnum\" > ${wd}/FSProcessing/batch${batch}/${hemi}.${moda}.batch${batch}.subbatch\${TASK_ID}.fwhm0.UKB.txt |; 
awk '{print \$1}' ${wd}/FSOUTPUT/batch${batch}/FSresults/${first}${hemi}.${moda}.fwhm0.fsaverage.asc >> ${wd}/FSProcessing/batch${batch}/${hemi}.${moda}.batch${batch}.subbatch\${TASK_ID}.fwhm0.UKB.txt |; 
for ID in \$(awk -F\",\" \"NR>0 {print \$1}\" ${rd}/ukb50815.20263.bulk.batch${batch}_subbatch\${TASK_ID}) |;
do |;
echo \${ID} |;
if [ -f ${wd}/FSOUTPUT/batch${batch}/FSresults/\${ID}/${hemi}.${moda}.fwhm0.fsaverage.asc ] |;
then |;
echo \${ID} > ${wd}/FSProcessing/batch${batch}/${hemi}.${moda}.\${TASK_ID}.temp.lta |;
awk '{print \$5}' ${wd}/FSOUTPUT/batch${batch}/FSresults/\${ID}/${hemi}.${moda}.fwhm0.fsaverage.asc >> ${wd}/FSProcessing/batch${batch}/${hemi}.${moda}.\${TASK_ID}.temp.lta |;
paste ${wd}/FSProcessing/batch${batch}/${hemi}.${moda}.batch${batch}.subbatch\${TASK_ID}.fwhm0.UKB.txt ${wd}/FSProcessing/batch${batch}/${hemi}.${moda}.\${TASK_ID}.temp.lta > ${wd}/FSProcessing/batch${batch}/${hemi}.${moda}.\${TASK_ID}.temp2.lta |;
cp ${wd}/FSProcessing/batch${batch}/${hemi}.${moda}.\${TASK_ID}.temp2.lta ${wd}/FSProcessing/batch${batch}/${hemi}.${moda}.batch${batch}.subbatch\${TASK_ID}.fwhm0.UKB.txt |;
fi |; done " 1 4G VertexData_UKB_${hemi}_${moda}_batch${batch} 10:00:00 "-array=0-7"
done
done
done



# 3) Put back together and remove temp files
bind="/network/lustre/iss02/ukbiobank/software" 
wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"
rd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant/Downloadfs" # reading directory (created above)
cd ${wd}/FSProcessing
qsub -I -l select=1:ncpus=1:mem=5GB -l walltime=05:00:00 -A UQ-IMB-CNSG

for batch in 43 # ...
do
wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant/FSProcessing/batch${batch}"
cd ${wd}
cp ${wd}/rh.thickness.batch${batch}.subbatch0.fwhm0.UKB.txt ${wd}/rh.thickness.batch${batch}.fwhm0.UKB.txt
cp ${wd}/lh.thickness.batch${batch}.subbatch0.fwhm0.UKB.txt ${wd}/lh.thickness.batch${batch}.fwhm0.UKB.txt
cp ${wd}/rh.area.batch${batch}.subbatch0.fwhm0.UKB.txt ${wd}/rh.area.batch${batch}.fwhm0.UKB.txt
cp ${wd}/lh.area.batch${batch}.subbatch0.fwhm0.UKB.txt ${wd}/lh.area.batch${batch}.fwhm0.UKB.txt

for moda in thickness area
do
for hemi in lh rh
do 
for subbatch in {1..7}
do
 echo ${subbatch}.${hemi}.${moda}.
# Get rid row names (1st column)
awk '{$1=""}1' ${wd}/${hemi}.${moda}.batch${batch}.subbatch${subbatch}.fwhm0.UKB.txt | awk '{$1=$1}1' > ${wd}/${hemi}.${moda}.batch${batch}.subbatch${subbatch}.fwhm0.UKB_noColNames.txt
# Paste to the combined file        
paste ${wd}/${hemi}.${moda}.batch${batch}.fwhm0.UKB.txt ${wd}/${hemi}.${moda}.batch${batch}.subbatch${subbatch}.fwhm0.UKB_noColNames.txt > ${wd}/${hemi}.${moda}.batch${batch}.fwhm0.UKB.temp.txt
cp ${wd}/${hemi}.${moda}.batch${batch}.fwhm0.UKB.temp.txt ${wd}/${hemi}.${moda}.batch${batch}.fwhm0.UKB.txt
rm ${wd}/*temp*
rm ${wd}/*_noColNames*
rm ${wd}/*subbatch*
done
done
done 
done

Sub cortical



for batch in 43
do
wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"
bind="/network/lustre/iss02/ukbiobank/software" 

# Convert tab file of IDs into csv (which ENIGMA shape package prefers)
cd ${wd}/FSOUTPUT/batch${batch}/ENIGMAshapeResults
echo "ID,V2" > ${wd}/FSProcessing/batch${batch}/groupfile_UKB.csv 
for d in `ls -d *` ; do
    echo ${d},V2 >> ${wd}/FSProcessing/batch${batch}/groupfile_UKB.csv
done

# Create all subcortical text files
cd ${wd}/FSProcessing/batch${batch}

${bind}/qsubshcom " groupfile=\"/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant/FSProcessing/batch${batch}/groupfile_UKB.csv\" |;
filename=\$(basename \"\${groupfile}\") |;
extension=\"\${filename##*.}\" |;
filename=\"\${filename%.*}\" |;
echo \${groupfile} |;
setROIS=\"10 11 12 13 17 18 26\" |;
${bind}/ENIGMA_shape/MedialDemonsShared/bin/raw_list2CSV_matrix ${wd}/FSProcessing/batch${batch}/\${filename}_LogJacs_lh.csv ${bind}/ENIGMA_shape/MedialDemonsShared/atlas GOF \${setROIS} LogJacs resliced_mesh \${groupfile} ${wd}/FSOUTPUT/batch${batch}/ENIGMAshapeResults |;
${bind}/ENIGMA_shape/MedialDemonsShared/bin/raw_list2CSV_matrix ${wd}/FSProcessing/batch${batch}/\${filename}_thick_lh.csv ${bind}/ENIGMA_shape/MedialDemonsShared/atlas GOF \${setROIS} thick resliced_mesh \${groupfile} ${wd}/FSOUTPUT/batch${batch}/ENIGMAshapeResults |;
setROIS=\"49 50 51 52 53 54 58\" |;
${bind}/ENIGMA_shape/MedialDemonsShared/bin/raw_list2CSV_matrix ${wd}/FSProcessing/batch${batch}/\${filename}_LogJacs_rh.csv ${bind}/ENIGMA_shape/MedialDemonsShared/atlas GOF \${setROIS} LogJacs resliced_mesh \${groupfile} ${wd}/FSOUTPUT/batch${batch}/ENIGMAshapeResults |;
${bind}/ENIGMA_shape/MedialDemonsShared/bin/raw_list2CSV_matrix ${wd}/FSProcessing/batch${batch}/\${filename}_thick_rh.csv ${bind}/ENIGMA_shape/MedialDemonsShared/atlas GOF \${setROIS} thick resliced_mesh \${groupfile} ${wd}/FSOUTPUT/batch${batch}/ENIGMAshapeResults |;
sed 's/,\+/ /g' ${wd}/FSProcessing/batch${batch}/\${filename}_LogJacs_lh.csv  > ${wd}/FSProcessing/batch${batch}/\${filename}_LogJacs_lh.txt |;
sed 's/,\+/ /g' ${wd}/FSProcessing/batch${batch}/\${filename}_LogJacs_rh.csv  > ${wd}/FSProcessing/batch${batch}/\${filename}_LogJacs_rh.txt |;
sed 's/,\+/ /g' ${wd}/FSProcessing/batch${batch}/\${filename}_thick_lh.csv  > ${wd}/FSProcessing/batch${batch}/\${filename}_thick_lh.txt |;
sed 's/,\+/ /g' ${wd}/FSProcessing/batch${batch}/\${filename}_thick_rh.csv  > ${wd}/FSProcessing/batch${batch}/\${filename}_thick_rh.txt |;
awk '\$2 != \"NaN\"' ${wd}/FSProcessing/batch${batch}/groupfile_UKB_LogJacs_lh.txt > ${wd}/FSProcessing/batch${batch}/lh.LogJacs.fwhm0.UKB.txt |;
awk '\$2 != \"NaN\"' ${wd}/FSProcessing/batch${batch}/groupfile_UKB_LogJacs_rh.txt > ${wd}/FSProcessing/batch${batch}/rh.LogJacs.fwhm0.UKB.txt |;
awk '\$2 != \"NaN\"' ${wd}/FSProcessing/batch${batch}/groupfile_UKB_thick_lh.txt > ${wd}/FSProcessing/batch${batch}/lh.thick.fwhm0.UKB.txt |;
awk '\$2 != \"NaN\"' ${wd}/FSProcessing/batch${batch}/groupfile_UKB_thick_rh.txt > ${wd}/FSProcessing/batch${batch}/rh.thick.fwhm0.UKB.txt |;
" 1 4G VertexData_Subcortical_UKB_batch${batch} 05:00:00 " "
done

Check dimensions of created files


wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"
bind="/network/lustre/iss02/ukbiobank/software" 

# Dimension batch files
for batch in 14
do
echo ${batch}
cd ${wd}/FSProcessing/batch${batch}

# Dimension merged file
awk '{print NF}' lh.area.batch${batch}.fwhm0.UKB.txt | sort -nu | tail -n 1 
awk '{print NF}' rh.area.batch${batch}.fwhm0.UKB.txt | sort -nu | tail -n 1 
awk '{print NF}' lh.thickness.batch${batch}.fwhm0.UKB.txt | sort -nu | tail -n 1 
awk '{print NF}' rh.thickness.batch${batch}.fwhm0.UKB.txt | sort -nu | tail -n 1 

# Check final files
cat lh.LogJacs.fwhm0.UKB.txt | wc -l 
cat rh.LogJacs.fwhm0.UKB.txt | wc -l 
cat lh.thick.fwhm0.UKB.txt | wc -l 
cat rh.thick.fwhm0.UKB.txt | wc -l 

# Number of columns
cat lh.area.batch${batch}.fwhm0.UKB.txt | wc -l 
awk '{print NF}' lh.LogJacs.fwhm0.UKB.txt | sort -nu | tail -n 1 
echo "Done bash ${bash}"

done

Import text files in OSCA


wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"
bind="/network/lustre/iss02/ukbiobank/software" 


mkdir -p ${wd}/BodFiles
od="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant/BodFilesFS"
cd ${wd}/BodFilesFS

for batch in 43
do
# Cortical
for hemi in lh rh
do
for moda in area thickness
do
${bind}/qsubshcom " ${bind}/osca --tefile ${wd}/FSProcessing/batch${batch}/${hemi}.${moda}.batch${batch}.fwhm0.UKB.txt --make-bod --no-fid --out ${od}/${hemi}.${moda}.batch${batch}.fwhm0.UKB " 1 10G ${hemi}_${moda}_MakeBod 10:00:00 "" 
done
done
done



# Subcortical - note different output name to match next section
wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"

cd ${wd}/BodFilesFS
for batch in {07..10} 
do
for hemi in lh rh
do
for moda in LogJacs thick
do
${bind}/qsubshcom " ${bind}/osca --efile ${wd}/FSProcessing/batch${batch}/${hemi}.${moda}.fwhm0.UKB.txt --make-bod --no-fid --out ${od}/${hemi}.${moda}.batch${batch}.fwhm0.UKB.vertexQC " 1 5G ${hemi}_${moda}_MakeBod 04:00:00 "" 
done
done 
done


cd ${wd}/BodFilesFS
for batch in 43
do
for hemi in lh rh
do
for moda in LogJacs thick
do
${bind}/osca --tefile ${wd}/FSProcessing/batch${batch}/${hemi}.${moda}.fwhm0.UKB.txt --make-bod --no-fid --out ${od}/${hemi}.${moda}.batch${batch}.fwhm0.UKB.vertexQC  
done
done 
done

#for subcortical values, data are transposed (.opi with id, .oii with probes) –> re transpose data in right way #convert bod in text, transpose, and re convert in bod


wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"
bind="/network/lustre/iss02/ukbiobank/software" 

od="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant/BodFilesFS"

cd ${wd}/BodFilesFS

for batch in {01..43}
do
for hemi in lh rh
do
for moda in thick LogJacs
do
${bind}/qsubshcom " ${bind}/osca --befile ${od}/${hemi}.${moda}.batch${batch}.fwhm0.UKB.vertexQC --make-tefile --no-fid --out ${od}/${hemi}.${moda}.batch${batch}.fwhm0.UKB.vertexQC.txt " 1 5G ${hemi}_${moda}_MakeFile 04:00:00 "" 
done
done 
done 

#re transpose to bodfiles transposed

for batch in {01..43}
do
for hemi in rh 
do
for moda in thick LogJacs
do
${bind}/qsubshcom "${bind}/osca --efile ${od}/${hemi}.${moda}.batch${batch}.fwhm0.UKB.vertexQC.txt --make-bod --no-fid --out ${od}/${hemi}.${moda}.batch${batch}.fwhm0.UKB.vertexQC_transp " 1 5G ${hemi}_${moda}_MakeBodTransp 04:00:00 "" 
done
done 
done

Delete OUTPUT folders that have been tarred up


for batch in 43
do
echo ${batch}
rm -r /network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant/FSOUTPUT/batch${batch}
rm -r /network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant/FSProcessing/batch${batch}

done

#exclude vertices outside of the cortex

wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"
bind="/network/lustre/iss02/ukbiobank/software" 

od="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant/BodFilesFS"
cd ${wd}/BodFilesFS


for batch in {01..43}
do
for hemi in lh rh
do
for moda in thickness area
do
${bind}/qsubshcom " "${bind}"/osca --befile "${wd}"/BodFilesFS/"${hemi}"."${moda}".batch${batch}.fwhm0.UKB --exclude-probe "${wd}"/BodFilesFS/VerticesToExclude_"${hemi}"_"${moda}"_Cortex.txt --make-bod --out "${wd}"/BodFilesFS/"${hemi}"."${moda}".batch${batch}.fwhm0.UKB.vertexQC " 1 10G ${hemi}_${moda}_excludeVertices 10:00:00 "" 
done
done 
done

#merging all bod from all batches

wd="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant"
bind="/network/lustre/iss02/ukbiobank/software" 

od="/network/lustre/iss02/ukbiobank/ukbiobank-remaining/elise.delzant/BodFilesFS"
cd ${wd}/BodFilesFS

for hemi in lh rh 
do
for moda in thick LogJacs
do
${bind}/qsubshcom "${bind}/osca --befile-flist mybodFS.flist.${hemi}.${moda} --make-bod --out ._${hemi}.${moda}.fwhm0.vertexQC " 1 50G ${hemi}_${moda}_merge_batch 10:00:00 "--partition=bigmem" 
done
done

#divide into main and replicate


wd="/network/iss/ukbiobank/ukbiobank-remaining/elise.delzant"
bind="/network/iss/ukbiobank/software" 

od="/network/iss/ukbiobank/ukbiobank-remaining/elise.delzant/BodFilesFS"

cd ${wd}/BodFilesFS

for hemi in lh 
do
for moda in thickness 
#for moda in 
do
for div in main replicate 
do
${bind}/qsubshcom " "${bind}"/osca --befile "${wd}"/BodFilesFS/Bod_${hemi}.${moda}.fwhm0.vertexQC --keep "${wd}"/BodFilesFSL/${div}_id.csv  --make-bod --no-fid --out "${wd}"/BodFilesFS/UKB_FS_${hemi}.${moda}.FinalBod.${div} " 4 128G Bod_${fsl}.${div} 48:00:00 "" 
done
done
done

#BRM

wd="/network/iss/ukbiobank/ukbiobank-remaining/elise.delzant"
bind="/network/iss/ukbiobank/software" 

cd ${wd}/BodFilesFS

for hemi in lh rh 
do
for moda in thickness area thick LogJacs
do
for div in replicate
do
${bind}/qsubshcom " ${bind}/osca --befile ${wd}/BodFilesFS/UKB_FS_${hemi}.${moda}.FinalBod.${div} --make-orm-bin --out ${wd}/BRM_Vol/UKB_FS_${hemi}.${moda}.FinalBod.${div}.BRM --thread-num 5 " 1 120G FSL_BRM_calculation 24:00:00 "" 
done 
done 
done

##Merging (left and right hemisphere for each modality)


wd="/network/iss/ukbiobank/ukbiobank-remaining/elise.delzant"
bind="/network/iss/ukbiobank/software" 

cd ${wd}/BRM_Vol

for div in main
do
for moda in thickness area 
do
${bind}/qsubshcom "${bind}/osca --multi-orm ${moda}_${div} --make-orm-bin --out UKB_FS_${moda}.FinalBod.${div}.BRM " 1 50G Merge_BRM_FS 10:00:00 " "
done 
done

#Merging all modalities


wd="/network/iss/ukbiobank/ukbiobank-remaining/elise.delzant"
bind="/network/iss/ukbiobank/software" 

cd ${wd}/BRM_Vol

for div in main replicate
do
${bind}/qsubshcom "${bind}/osca --multi-orm all_moda_fs_${div} --make-orm-bin --out UKB_FS_all_moda.FinalBod.${div}.BRM " 1 50G Merge_BRM_FS 10:00:00 ""
done

A work by by Elise Delzant

FreeSurfer pipeline

by Elise Delzant - 31 July 2025