Dear Afni community,
I have been trying to run an analysis in these last few days in which I have an AM1 regressor treated as being part of the baseline model via the -stim_base option in 3dDeconvolve. My understanding is that only AM1 and AM2 regressors can use the dmUBLOCK and dmBLOCK basis functions. Is this correct?
Here is the error I am getting:
** ERROR: ‘-stim_base 1’ illegal with ‘-stim_times_AM1’
** FATAL ERROR: Can’t continue after above problems!
My understanding is that 3dDeconvolve is telling that amplitude modulated/duration modulated regressors can’t be treated as being part of the baseline model. Is this correct? And if so, why not?
From what I recall, your points are correct, that _AM*
is required for dmBLOCK, and that those cannot go
into the baseline model. The reason for the latter I
am not sure of, except that it is surely because of
where in the code the AM regressors are generated.
But to flip it around, why do you really care to put
them in the baseline mode? The only effects of
that would be:
the Full_Fstat would include them (not the partials)
the default would be to give output volumes with
those betas and stats
It seems likely that you do not care about 1, and
it seems likely that you might actually prefer 2,
i.e. seeing the results.
So would you please clarify why you want them
in the baseline model?
Thank you for your response.
If I understand correctly, whether or not a regressor is included in the baseline model does not change either the beta weights or the partial t-statistics associated with all other regressors. Is this correct?
If so, I do think I agree with you and wouldn’t really see a good reason to mind this point.