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

[Ingrid Nieuwenhuis]

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 [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Andrew Smart
Sent: Friday, August 24, 2007 6:41 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: [FIELDTRIP] problem w/ cfg.highlight using topoplot to show samples
in sig clusters

Hi,
I have run a cluster analysis comparing two conditions on channel data and
have 1 pos significant
cluster and 1 negative significant cluster. When I run the following code
from the tutorial to plot:

UNvsID=grandavgUN;
UNvsID.avg=UNvsID.avg-grandavgID.avg;

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

j = [0:0.05:0.5];
m = [1:15:301];

for k=1:10;
subplot(4,5,k);
cfg=[];
cfg.xlim=[j(k) j(k+1)];
pos_int = mean(pos(:,m(k):m(k+1))')';
neg_int = mean(neg(:,m(k):m(k+1))')';
cfg.highlight=find(pos_int==1|neg_int==-1);
cfg.comment = 'xlim';
cfg.commentpos = 'title';
cfg.layout = 'CTF275.lay';
topoplotER(cfg,UNvsID)
end

the raw effect is plotting but the samples belonging to the significant
clusters are not highlighted,
as on the tutorial page. So I can't tell when and where the effect is.

 When looking at the topoplot function cfg.highlight does not appear to be
an option anywhere.
Do I need a newer version of Fieldtrip? The one I am using now is from
2007/08/01.

Thanks for any help!
andy

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FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
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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/fcdonders/fieldtrip.