Your script says:
# EDIT BELOW: this is the root directory where the patient files are
my $patientFileRoot = "/mnt/images/patient";
I don't think that directory is available on your new system. You need to locate the /images/patient directory and edit the path to it.
"mnt/" usually means you've mounted something (like a cd) and I think you aren't doing that.
BTW
Further down in the script you have another place to edit:
# now get patients and start calculating file counts and sizes
# EDIT BELOW: change the name of the file to october to do October
open (PATIENTS, "september.csv") or die $!;
#open (PATIENTS, "october.csv") or die $!;
You might want to check those file names are correct too.
-Sidney