problem w/ cfg.highlight using topoplot to show samples in sig clusters

Andrew Smart at NYU.EDU
Wed Aug 29 17:41:05 CEST 2007

Hi Ingrid,
Thank you for the answer.  The output of
cfg.highlight = find(pos_int==1|neg_int==-1) is in fact empty as you say, so
this might depend on giving the wrong sampling frequency in m? The data I
have is sampled at 600. So should m be then something like m= [1:30:600] if
my time window of interst is 0-500 ms?

I did find topoplot eventually and tried the different settings but I think the
problem is as you suggest with the inputs to the plot.

I use the within-subjects input to the statistics function given in the tutorial as:

cfg = []; = {'MEG'};
cfg.latency = [0.0 0.5];                % so the effect shouldn't be outside this
                                                 % time interval, correct?
cfg.method = 'montecarlo';
cfg.statistic = 'depsamplesT';
cfg.clusteralpha = 0.05;
cfg.clusterstatistic = 'maxsum';
cfg.minnbchan = 2;
cfg.tail = 0;
cfg.clustertail = 0;
cfg.alpha = 0.05;
cfg.numrandomization = 500;
cfg.layout = 'CTF275.lay';

subj = 16;
for i = 1:subj
  design(1,i) = i;
for i = 1:subj
  design(1,subj+i) = i;
design(2,1:subj)        = 1;
design(2,subj+1:2*subj) = 2;   = design;
cfg.uvar  = 1;
cfg.ivar  = 2;

[stat] = timelockstatistics(cfg, grandavgID, grandavgUN);

Thank you for your help!


----- Original Message -----
From: Ingrid Nieuwenhuis <ingrid.nieuwenhuis at FCDONDERS.RU.NL>
Date: Wednesday, August 29, 2007 5:12 am
Subject: Re: [FIELDTRIP] problem w/ cfg.highlight using topoplot to show
samples in sig clusters

> Hi Andrew,
> You can find the option cfg.highlight in the function topoplot.m, this
> function is called by topoplotER (also by topoplotTFR by the way). It
> should
> contain the channel numbers which you want to highlight.
> Why your plot doesn't give any highlighted sensors is hard to say without
> knowing your data (what did you give in to timelockstatistics with which
> cfg).
> - It could be that the time you plot (0:0.05:0.5) does not contain the
> clusters
> - It could be the specification of m [1:15:301], this is exactly
> copied from
> the tutorial, but it is based on the sample frequency of the data used
> there. In the tutorial a second of data is used, cut up in 21 pieces from
> 0:0.05:1 and that data has a sample frequency of 301 also cut up in 21
> pieces 1:15:301. You should adjust m to you own time settings and sample
> frequency.
> - cfg.highlight = find(pos_int==1|neg_int==-1), what is the outcome of
> this?
> For the highlighting to work it should contain the sensor numbers to be
> highlighted. If your m is not specified correctly I would guess that pos_int
> and neg_int are not specified correctly and cfg.highlight turnes up empty
> and therefore no highlights are plotted.
> Hope this give you some ideas to find out what's wrong.
> Good luck,
> Ingrid
> -----Original Message-----
> From: FieldTrip discussion list [

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