After I run my preprocessing through my university's HPC (no errors, everything goes smoothly), save the project, and return at a later time, Conn throws an error saying that my participant .nii files no longer exist, and prompts me to identify each participants' anat files manually. Participants' .nii.gz files are still in their expected folders, although their .nii files are indeed gone. I made no changes to the project between when I saved and tried to open the project later. I can always rerun but it's very frustrating that seemingly at random I have to restart the whole process if I save to take a break. 

Can anyone tell me if I'm missing something? I would ideally like to be able to save and actually use that saved file later on without all of my participant files going "missing"! Or if I can even find a way to tell conn that if the .nii files aren't there to use the .nii.gz files that would work.

Thanks!