Hi Christine,
Just to add to Colm's good example, there are 2 things that go wrong in your example, though Dimon could be updated to handle them.
One is that the GERT_Reco scripts use a simple 'mkdir' command to make directories. If intermediate directories are needed, that would fail. It can be updated to include the -p option.
The other is specifying a NIFTI prefix is not reconciled with outdir and -gert_write_as_nifti.
I will fix both of those things and run a new build tonight.
Thanks,
- rick
