Rick:
The test case is this: We want 3dWarp to repeat the exact operation that was performed by 3dTagalign, using the matvec file produced by 3dTagalign.
If I read your reply correctly (and I'm unsure about that), you seem to be saying that the appropriate flag for this would be in2out, in agreement with me.
If so, you are contradicting the -helps for two or more AFNI programs, which say to use out2in.
That's the problem.
Since the referents of "in" and "out" to me seem arbitrary here, I'm not sure what it's *supposed* to do... (it's just OptionA and OptionB)... but this sure looks like the helps don't match what you say is the intent here.
Graham
