[FieldTrip] Granger Causality with ft_connectivity_analysis

Helen Wieffering helen.wieffering at gmail.com
Fri Oct 23 23:53:48 CEST 2015

Hi Per,

Thanks for your suggestion, and I'm sorry for my (much) delayed reply.

I've read the paper you mentioned - it seems this could be promising for my
work, too. I hadn't considered the non-parametric approach.

Could you give me more detail on the pre-processing steps you took and the
parameters you're using with the fieldtrip connectivity functions? I'd love
to look at the scripts you're using, too, if at all possible.

Thanks again.

Helen Wieffering
Bowdoin College

On Wed, Oct 7, 2015 at 4:55 PM, Per Arnold Lysne <lysne at unm.edu> wrote:

> Hi Helen,
>     I am having good luck with ft_connectivity_analysis in MEG using the
> nonparametric Granger approach of Dhamala, Rangarajan & Ding, 2008,
> Neuroimage and Physical Review letters.
>     Thanks,
> Per Lysne
> University of New Mexico
> lysne at unm.edu
> -----Original Message-----
> From: Helen Wieffering
> Sent: Oct 7, 2015 8:59 AM
> To: FieldTrip discussion list
> Subject: [FieldTrip] Granger Causality with ft_connectivity_analysis
> Dear FieldTrip users,
> I'm writing to see if any one out there has had success with computing
> Granger causality measures in FieldTrip. We have been working toward making
> this analysis possible with our EEG data and have now reached the final
> stages.
> However, we find that ft_connectivity_analysis (and
> ft_connectivity_granger for that matter) offers little guidance on how to
> achieve a good mvar model fit. For example, the function asks the user to
> specify the model order without offering tests for whiteness, stationarity,
> or consistency. It seems that Fieldtrip calls on the BSMART toolbox to
> perform these operations, which further confuses me given that BSMART
> itself offers these model validation tests. Yet they don't seem to ever be
> called upon by FieldTrip.
> We've considered using the BSMART toolbox separately from FieldTrip, yet
> the toolbox website is rather outdated and the functions are only
> compatible through 2008 Matlab - seems like a headache. But without tools
> for validating the mvar model, we can't be confident of any GC results
> achieved through FieldTrip.
> Are there perhaps further connectivity tools in FieldTrip that I've
> overlooked? Or is it worth looking into other toolboxes? We've also
> considered SIFT and the MVGC toolbox, but would love to keep working with
> FieldTrip if possible.
> If anyone can offer advice, or connect me with someone knowledgeable in
> this area, I'd love to know.
> Thanks very much,
> Helen Wieffering
> Bowdoin College
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> fieldtrip at donders.ru.nl
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