[RESOLVED] runQC seems to have different issues with setting paths

Description:

When running the runQC command there are several issues with setting paths of either the input data or the output files. For example, input images cannot be found because they are searched for in the wrong folder (e.g. “PATH TO FILE: /gpfs/loomis/pi/n3/Studies/MBLab/MMI/subjects/MNINonLinear”). The output path, if not explicitly set, defaults to the home directory, instead of the study folder. The command also generates folders that are missing from the general Qunex folder structure, but are not used for the purpose of that command and are thus unnecessary.

Call:

qunex runQC --sessionsfolder="/gpfs/loomis/pi/n3/Studies/MBLab/MMI/subjects" --sessions=“Z1VPF” --modality=“T1w” --outpath="/gpfs/loomis/pi/n3/Studies/MBLab/MMI/subjects/QC/T1w" --overwrite=“no”

Logs:

runQC_log_Z1VPF-2.txt (10.6 KB)

Hi Nina, the developers are currently working on this issue. We will let you know once the issue is resolved.

Hello, Nina,

I am letting you know that the issue has been resolved.