Ahoi hoi @mri,
I’m not sure, but I think, one option could be to define a function node that takes
all unzipped .nii as input (waiting till all are there) and then passes them to flirt.
With that it would act as a dummy function/node that triggers flirt only after all subjects’ data were unzipped.
Your question goes into the direction of what was asked here, with nipype being a “dataflow framework”.
HTH, cheers, Peer