Qbatch tips - GarzaLab/Documentation GitHub Wiki

Run Maget-QC.sh using qbatch on Scinet

Download the Maget-QC.sh script, put it in the MAGET folder, then do a loop and make it a text file, such as this:

for i in input/subjects/brains/*.mnc; do file=$(basename $i); echo ./MAGeT-QC.sh ${i} output/fusion/majority_vote/${file%.*}_labels.mnc Maget-QC/${file%.*}.jpg;done > maget_qc_joblist

Then run it as a qbatch job:

qbatch -N cann_colin_qc --walltime=1:00:00 maget_qc_joblist