Freqstatistics Yields Zero Significant Clusters?

Michael Wibral wibral at BIC.UNI-FRANKFURT.DE
Tue Jun 9 15:05:11 CEST 2009


Hi Charles,

I agree with Eric. You might try to define a much smaller neighbour distance. The reason for this may be that BESA sometimes uses [cm] and sometimes [m] - so if all your neighbour positions are given im [m] aand you specify the maximum distance in [cm], the all channels are neighbours of all other channels. I remeber that some of the fieldtrip scripts in the wiki multiplied the .pnt field by 10 or 100 after import from BESA and before proceeding. A note on the side: beware of a "ms" and "s" problem as well. That means check all .time fields in your fieldtrip structures for plausibility.

Hope this helps,
Michael



> -----Urspr√ľngliche Nachricht-----
> Von: "Eric Maris" <e.maris at DONDERS.RU.NL>
> Gesendet: 08.06.09 17:03:03
> An: FIELDTRIP at NIC.SURFNET.NL
> Betreff: Re: [FIELDTRIP] Freqstatistics Yields Zero Significant Clusters?


> Hi Charles,
> 
> 
> > We have modified the code based on your suggestions and I think we're very
> > close now. This is our most recent output:
> > 
> > -------------------------------------
> > reading power on 81 channels
> > not computing grand average, but keeping individual power for 11 subjects
> > not computing grand average, but keeping individual power for 11 subjects
> > selected 81 channels
> > selected 6 time bins
> > selected 4 frequency bins
> > Warning: PACK can only be used from the MATLAB command line.
> > > In fieldtrip\private\prepare_timefreq_data at 310
> >   In fieldtrip\private\statistics_wrapper at 206
> >   In freqstatistics at 132
> >   In CMCWM2_std81_junk_with at 144
> > Obtaining the electrode configuration from the configuration.
> > there are on average 83.0 neighbours per channel
> 
> 83.0 neighbours per channel does not make sense. For EEG-channels this
> number typically is 4 and for MEG-channels it is typically 6. Have a look at
> the neighbourhood geometry structure that is constructed by freqstatistics.
> I guess this structure is far too wide (a channel is considered a neighbour
> of almost every other channel).
> 
> 
> Best,
> 
> Eric
> 
> 
> 
> 
> 
> 
> 
> > using "statistics_montecarlo" for the statistical testing
> > using "statfun_indepsamplesT" for the single-sample statistics
> > constructing randomized design
> > total number of measurements     = 22
> > total number of variables        = 2
> > number of independent variables  = 1
> > number of unit variables         = 1
> > number of within-cell variables = 0
> > number of control variables      = 0
> > using a permutation resampling approach
> > repeated measurement in variable 1 over 22 levels
> > number of repeated measurements in each level is 1 1 1 1 1 1 1 1 1 1 1 1 1
> 1
> > 1 1 1 1 1 1 1 1
> > computing a parmetric threshold for clustering
> > estimated time per randomization is 0 seconds
> > found 2 positive clusters in observed data
> > found 1 negative clusters in observed data
> > using a cluster-based method for multiple comparison correction
> > the returned probabilities and the thresholded mask are corrected for
> > multiple comparisons
> > ??? Assignment has more non-singleton rhs dimensions than non-singleton
> > subscripts
> > 
> > Error in ==> clusterplot at 91
> >     sigposCLM(:,:,iPos) = (posCLM == sigpos(iPos));
> > 
> > Error in ==> CMCWM2_std81_junk_with at 153
> > clusterplot (cfg, stat);
> > 
> > -----------------
> > 
> > We do keep running into this error with clusterplot. Which we have as
> follows:
> > 
> > cfg = [];
> > cfg.zlim = [-6 6];
> > cfg.alpha = 0.05;
> > clusterplot(cfg, stat);
> > 
> > It crashes on the last line. Does anyone have any ideas where we might be
> > going wrong here?
> > 
> > Cheers,
> > 
> > Charles
> > 
> > On Sat, 6 Jun 2009 09:04:43 +0200, Eric Maris <e.maris at DONDERS.RU.NL>
> > wrote:
> > 
> > >Hi Charles,
> > >
> > >
> > >
> > >Although I'm not 100 percent sure that this is the cause of your
> problems,
> > >the way you specify the unit of observation is definitely wrong. You have
> 22
> > >units of observations (i.c., subjects) so the first row of cfg.design
> must
> > >be [1 2 ... 22; ... ]
> > >
> > >Also, did you check whether cfg.design is a 2-by-22 array? In the lines
> > >below, a semicolon seems to be missing.
> > >
> > >> cfg.design           = [1 2 3 4 5 6 7 8 9 10 11 1 2 3 4 5 6 7 8 9 10 11
> %
> > >> subject number is 1-11 males and 1-11 females
> > >>                         1 1 1 1 1 1 1 1 1 1  1  2 2 2 2 2 2 2 2 2 2
> 2]; %
> > >> condition number with 1 being males and 2 being females
> > >>
> > >> cfg.uvar = 1;                                   % "subject" is unit of
> > >> observation
> > >> cfg.ivar = 2;                                   % "condition" is the
> > >> independent variable
> > >
> > >
> > >Good luck,
> > >
> > >
> > >dr. Eric Maris
> > >Donders Institute for Brain, Cognition and Behavior
> > >Center for Cognition and F.C. Donders Center for Cognitive Neuroimaging
> > >Radboud University
> > >P.O. Box 9104
> > >6500 HE Nijmegen
> > >The Netherlands
> > >T:+31 24 3612651
> > >F:+31 24 3616066
> > >E: e.maris at donders.ru.nl
> > >
> > >MSc Cognitive Neuroscience: www.ru.nl/master/cns/
> > >
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users of the
> FieldTrip
> > toolbox, to share experiences and to discuss new ideas for MEG and EEG
> analysis.
> > See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/neuroimaging/fieldtrip.
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
> 



----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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