[FieldTrip] Neuromag sensor level stats

[Eelke Spaak]

Hi Peter,

The cluster-based permutation test by itself is fully corrected for
multiple comparisons. You mention "cluster based t-tests", but the
exact test statistic (in your case, t) is irrelevant for this method.
>From your comment I think you already understand this, but I thought
it good to point out nonetheless :)

Strictly speaking, when doing several cluster-based permutation tests,
the cluster-level p-values you get out are uncorrected with respect to
the several different tests, so actually I think it would be formally
appropriate to correct them (with the number of cluster tests, *not*
number of clusters of course), using Bonferroni or Holm-Bonferroni
correction or so. I don't think this is commonly done, though.

Best,
Eelke

On 25 September 2012 02:37, Peter Goodin <pgoodin at swin.edu.au> wrote:
> Thanks very much for the responses Stephan and Jörn!
>
>
>
> One last question if possible Jörn. In your opinion, will doing several (at
> the most 5) cluster based t-tests affect the validity of permutation method
> testing to control for multiple comparisons? Would being more conservative
> regarding my alpha (for example a combination of permutation AND Bonferroni)
> possibly alleviate this?
>
>
> Thanks again for the responses,
>
>
>
> Peter.
>
>
>
> From: fieldtrip-bounces at science.ru.nl
> [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of "Jörn M. Horschig"
> Sent: Monday, 24 September 2012 10:15 PM
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] Neuromag sensor level stats
>
>
>
> Dear Peter,
>
> regarding your first question, most people here at the Donders actually
> repair bad channels. When computing the grandaverage over subjects or doing
> some statistics across subjects, only those channels which are in common for
> all datasets are used. Thus, if having different channels damaged/rejected
> per subjects, you can end up with a fairly low amount of channels. But, in
> the end it depends pretty much on what channels you reject wrt your
> hypothesis, e.g. having few occipital channels while being interested in
> motor regions won't constitute a big problem, so no need to interpolate. I
> leave the question whether it's a correct thing to do up to you (imho: I
> wouldn't worry too much about it).
>
> Regarding your third question: In FieldTrip you can only compare two
> conditions directly (at least when doing cluster-based permutation testing).
> Also, any interaction needs to be setup manually.
>
> Best,
> Jörn
>
> On 9/23/2012 3:14 PM, Peter Goodin wrote:
>
> Hi Fieldtrippers,
>
>
>
> I'm at a stage where I'd like to do statistical analysis on my ERF neuromag
> data, but don't really know where to begin. I'd like to do a cluster
> analysis, but the tutorial material is for a CTF system. I'm using a
> neuromag 306 channel which complicates matters somewhat due to the different
> sensor types. I've searched the mailing list but can't find any solid
> answers / example scripts.
>
>
>
> The most pressing questions I have are:
>
>
>
> 1. Despite running the data through maxfilter and entering in the bad
> channels, occasionally one gets through (not the same one). I've used
> Fieldtrip's repairchannel function on the data, making sure to replace the
> channel only with like sensor neighbouring sensors. While I know this is a
> common method for fixing bad channels in EEG, does the same hold for MEG due
> to non-existent smearing of the signal? Is it best to keep the fixed
> channel(s) or just remove them from the stats analysis across all
> participants?
>
>
>
> 2. Given the three sensor types on the neuromag system, do I need to run
> three different cluster analyses (one for mags, one for xgrads, one for
> ygrads), each time specifying like sensor neighbours? Alternatively, If I'm
> not interested in the mags data, can I just  run one using the data from the
> combined gradiometers?
>
>
>
> 3. When examining for group x condition effects, would I use a three row
> design matrix with row 1 containing group, row 2 containing participants and
> row 3 conditions?
>
>
>
> Thanks for any help,
>
>
>
> Peter
>
>
>
>
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>
>
> --
>
> Jörn M. Horschig
>
> PhD Student
>
> Donders Institute for Brain, Cognition and Behaviour
>
> Centre for Cognitive Neuroimaging
>
> Radboud University Nijmegen
>
> Neuronal Oscillations Group
>
> FieldTrip Development Team
>
>
>
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>
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>
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>
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>
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>
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>
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>
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>
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