I have a followup to the response below concerning scaling the PEs to
account for the amplitude of the columns in the design.mat.

Namely, if FILM has run correction for auto-correlations, then isn't
there technically a different design matrix for every voxel? So wouldn't
the PE corrections would need to be voxel-wise? But there is only one
design.mat written out, implying global auto-correlation correction.
What is  the right way to re-scale the PEs?


On Thu, 9 Dec 2004 01:26:31 +0000, Stephen Smith
<[log in to unmask]> wrote:

>Hi - in order to interpret the absolute size of estimated PE values, you
>need to first multiply them by the peak-to-peak height in the model
>look inside design.mat) - after doing this, regardless of the
>type, you know the fitted peak-to-peak height. In none of this, at this
>point, are things normalised into percentages (etc.).
>Cheers, Steve
>On Wed, 8 Dec 2004, Ramapriyan Pratiwadi wrote:
>&gt; Hi,
>&gt; We recently ran an analysis using the FIR basis set, rather than
the the
>&gt; double-gamma HRF.  To our surpise, the range of values for the
pe images
>&gt; were much much lower than expected; in fact, they look like
>&gt; signal change.  And when the betas for the basis set were
graphed, they
>&gt; indeed looked like a typical HRF.
>&gt; Do the pe images need to be scaled in some way, or are they
already in
>&gt; percent deviation from baseline.
>&gt; Thanks,
>&gt; Ram
>&gt; ------------------------------------
>&gt; Ram Pratiwadi
>&gt; Research Assistant
>&gt; University of Pennsylvania, Brain Behavior Laboratory
>&gt; --
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> Stephen M. Smith  DPhil
> Associate Director, FMRIB and Analysis Research Coordinator
> Oxford University Centre for Functional MRI of the Brain
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726  (fax 222717)
> [log in to unmask]