[FieldTrip] Neuromag sensor level stats

"Jörn M. Horschig" jm.horschig at donders.ru.nl
Mon Sep 24 14:15:05 CEST 2012

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.


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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> fieldtrip at donders.ru.nl
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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

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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