[pymvpa] events with model of bold response?

Michael Hanke michael.hanke at gmail.com
Mon Nov 1 14:48:32 UTC 2010


On Mon, Nov 01, 2010 at 11:35:57AM +0100, Brian Murphy wrote:
> Hi,
> I see that there are several handy ways to get an aggregate BOLD
> measure for each fMRI event: transform_with_boxcar, BoxCarMapper,
> and ERNiftiDataset. And by default they use a simple average of a
> fixed number of volumes. Is there a way to make them use another
> averaging method (transform_with_boxcar at least seems to allow
> this), and if so, does PyMVPA or any other part of NeuroDebian have
> a function for modelling the BOLD response?

You can indeed provide a custom function to process the boxcars. There
is GLM (a very very very basic implementation) to do fitting and stuff
like {single,double}GammaHRF() to create a design. There is also FslGLMDesign()
to load an existing GLM setup from FSL is you happen to have one.

So depending on what exactly you want to achieve (per event/run/subject
betas) you should be able to get it done. Of course you can also craft a
modeling function with NiPy and feed that into transformWithBoxcar(), or
you could also use NiPy or some other toolkit to do the full modelling
and only load beta image into PyMVPA for further processing.



GPG key: 4096R/7FFB9E9B Michael Hanke

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