Hi Archie,
If this is not a misunderstanding with respect to the operation of for_each, these files should correspond with what is generated at step 16:
for_each * : fixelcorrespondence IN/fixel_in_template_space/fd.mif ../template/fixel_mask ../template/fd PRE.mif
It looks different because the (current) interface to fixelcorrespondence takes output directory and file names separately, and a different for_each substitution string is used. But if the files are genuinely not there, we’d need to look closer.
Rob