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> Re (3), I might have been unclear in formulating my question.  I
> always generate flow fields from rc* files, but I was unsure if flow
> fields should be applied to images (eg T1 or Jacobians from HDW)
> aligned with rc* files or images aligned to c* files.  The guide seems
> to imply rc* files, but it seems that in actuality it is c* files.  

Use images aligned with c* files. I guess I'll have to take a look at
the guide to try to make it a bit more clear.

Best regards,
-John

-- 
John Ashburner <[log in to unmask]>