single modality at a time

[akhanf]

• change modality from a list to a string
• removes modality wildcard from all (except work tar file)
• changes seg_{modality} and surf_{modality} to seg_ and surf_ (allowing
  for further refactoring)
• T2w workflow updated and dry-run tested, others are WIP

[akhanf]

ok this looks good to review and merge in -- I didn't do any other refactoring here (except for renaming seg_{modality} and surf_{modality} to seg and surf.

[jordandekraker]

This might be a good place for one more thing - perhaps we should change the default modality to T1w? This seems to be most common plus in many cases it seems to work better

[akhanf]

Yeah I agree, I think defaulting to T2w doesn't make sense anymore..

I am thinking we should just make --modality a required argument and not have any default at all. That avoids any surprises in changing the default, and is probably safer since we are no longer allowing multiple different modalities in the same folder..

[jordandekraker]

Ah didn't realize you updates the name. warps.smk will need 'seg_{modality}' replaces with just 'seg'

[akhanf]

ya I updated those already with a recent merge of master.. I'll fix the remaining conflicts now (after merging in neonatal) then merge this in