When running the runQC command on hcp folders with a specific suffix (specified with the parameter --hcp_suffix), the created images do not match the results opened manually in FreeSurfer. The problem is probably that the command takes images from the hcp folder without any suffix (i.e. as if the --hcp_suffix is not taken into account). Otherwise, the command is run successfully and there is no sign of errors in log files, which makes this error very difficult to catch.
study=/gpfs/loomis/pi/n3/Studies/MBLab/sWM
for session in `ls -d $study/subjects/OP*`
do
subject=`basename $session`
qunex runQC --subjectsfolder=$study/subjects --subjects=$subject --hcp_suffix="_sulc" --modality="T1w" --overwrite="no" --scheduler="SLURM,jobname=QC,time=04:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=4000,partition=pi_anticevic"
qunex runQC --subjectsfolder=$study/subjects --subjects=$subject --hcp_suffix="_sulc" --modality="T2w" --overwrite="no" --scheduler="SLURM,jobname=QC,time=04:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=4000,partition=pi_anticevic"
qunex runQC --subjectsfolder=$study/subjects --subjects=$subject --hcp_suffix="_sulc" --modality="myelin" --overwrite="no" --scheduler="SLURM,jobname=QC,time=04:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=4000,partition=pi_anticevic"
done
done