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

Ingrid Nieuwenhuis ingrid.nieuwenhuis at FCDONDERS.RU.NL
Thu Aug 30 15:28:59 CEST 2007

```Hi Andrew,

- where does this size come from if my sample rate is 600?:
The size 267x301 means 267 channels x 301 samples. You have 301 samples
because your latency in timelockanalysis was cfg.latency = [0.0 0.5]; so
that's 301 samples with sample rate 600

Plotting the output from the randomization can be quite tricky, because you
have 301 moments in time where you can have a cluster. In the tutorial a
trick was used. There they also had 301 time points, but a sample rate of
300 -> spanning one second. If you exactly want to know where the clusters
are you would have to plot all the 301 time points. Because that doesn't
make sense they average over 50 millisecond time windows. If for instance
k=10 -> pos_int = mean(pos(:,m(k):m(k+1))')' -> an average is made over
samples 136-151 time is 0.45-0.5s giving the 10th plot in the figure. Only
those sensors that are part of the cluster for this whole time window (all
15 time points) give out a mean of 1 or -1 and are plotted. In the tutorial
data the cluster was present over a long time window in many sensors,
therefore there were many sensors with 1 or -1.

For your data this doesn't work, but you do have significant clusters.

"I can find the elements of pos and neg that = 1 and = -1 respectively.
elements =1 are spread out between roughly pos(59:168,149:172) and =-1
between neg(152:240,242:270)"

For instance this means that the positive clusters are in channel 59:168 at
time points 149:172, with a sample rate of 600 this means from 0.248 to
0.287 seconds. You should adjust the loop in such a way that you put the
settings that they fit your data. So for instance make the time resolution
higher (by adjusting j and m) since you have clusters that are short lived
in time, and to have not to many plots, plot around the time where you know

Good luck again.
Ingrid

-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Andrew Smart
Sent: Wednesday, August 29, 2007 8:02 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] problem w/ cfg.highlight using topoplot to show
samples in sig clusters

Hi Ingrid again,
Inspecting the variables more I find that the output of the
timelockstatistics on
my data gives:
28 pos clusters and 36 neg clusters (1 significant pos cluster and 1 sig neg

cluster)

and posclusterslabelmat and negclusterslabelmet as 267x301 (where does this
size come from if my sample rate is 600?)

then using
pos = stat.posclusterslabelmat==1;
neg = (stat.negclusterslabelmat==1)*(-1);

pos and neg are obviously 267x301,
and I can find the elements of pos and neg that = 1 and = -1 respectively.
elements =1 are spread out between roughly pos(59:168,149:172) and =-1
between neg(152:240,242:270).

however, using

pos_int = mean(pos(:,m(k):m(k+1))')';
neg_int = mean(neg(:,m(k):m(k+1))')';

in the for loop, gives pos_int as 267x1 but all the elements are zeros.

and in neg_int some elements are values like -0.1667 for example.

so for the highlight to work do the values in pos_int and neg_int have to be

either 1 or -1?

i have tried various parameters in m and but nothing i have tried seems to
work. i am stuck!

thanks!
andy

----- 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
To: FIELDTRIP at NIC.SURFNET.NL

> 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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