Clusterplot not highlighting clusters & average layout file

[Manish Saggar]

Ingrid, thanks for replying back.

Apologies for lack of information.

Clusterplot is plotting clusters fine most of the times, but in some
cases it doesn't choose to highlight markers. I have attached two such
images with this email.

I do not get any errors or warnings. In fact the command window in
matlab says, cluster found (with some prob and highlighter sign) and
then the plot doesn't contain any highlighting.
Initially I thought that my layout file might be messing it up or
something, or may be I need to take an average layout file for group
analysis (since cap size and electrode digitization varies for each
subject).

Then I put debug points in the code and found out that at line 235 the
list cell (used to denote highlighted points) is empty. I am a novice
so please forgive if what I am suggesting is dumb here, but I think
when cluster plot is searching for significant clusters it is only
looking into first column (which could correspond to first frequency
in band) if one cluster is found by freqstats. It might be that in the
code you guys are sorting columns and I might have missed it. But I
thought I should clear this with you.

In another thread you have mentioned to someone that their time limits
might not be precise enough to get the clusers highlighted (https://listserv.surfnet.nl/scripts/wa.cgi?A2=ind0709&L=FIELDTRIP&P=R680
). But they were doing time-freq analysis and I am just doing freq-
representations. So should I use freqstats on each freq separately ?

On a side note, when I run freqstats on my data (with 88 channels)
command line says '89 neighbors per channel found'. I am a little
confused with this. First since I only have less than 88 channels in
the data and second since it should only consider a lower number for
neighbor distance, right? and how can I change it?

Thanks a ton in advance,
Manish

On May 13, 2009, at 2:10 AM, Ingrid Nieuwenhuis wrote:

> Dear Manish,
>
> You give a bit too few information to be able to figure out what
> could be
> the problem with clusterplot. After calling clusterplot, clusterplot
> gives
> information on which clusters it finds. Does the function find any
> clusters?
> Does the .mask field of the structure that comes out of freqstatistics
> contain any ones? Is everything else plotted normally? Do you get
> any errors
> or warnings?
>
> I'm not familiar with BESA layout files, but assuming that all
> layout files
> are similar over subjects, I think it is fine to just use an
> individual
> subject's layout file.
>
> Hope this helps,
> Best Ingrid
>
>
>>  ---Original Message-----
>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
>> Behalf Of Manish Saggar
>> Sent: Tuesday, May 12, 2009 10:17 AM
>> To: FIELDTRIP at NIC.SURFNET.NL
>> Subject: [FIELDTRIP] Clusterplot not highlighting clusters & average
>> layout file
>>
>> All,
>>
>> I have a question regarding clusterplot function. I am doing a
>> within-subject analysis.
>> The experimental design that I have is as follows, there are three
>> conditions C1, C2 and C3. Each condition is of 1 min duration (e.g.
>> rest with eyes open for 1 min).
>>
>> Now I am comparing grandaverage of freq representation of a set of
>> subjects for C2 with C1 etc. FreqStatistics is running just fine
>> creating significant (<0.025 alpha, for 2-tailed test) clusters
>> (positive). Now the problem is that when I try to plot the location
>> of
>> this cluster using clusterplot it doesn't show any highlighted
>> channels. Any ideas why that is happening?
>>
>> Another question is that since I am using grandaverages of freq
>> representation, what should I use for layout file (using BESA sfp
>> file
>> here). I have individual subject layout files. Currently I am just
>> giving any file from one of the subjects. Since, I noticed that
>> FreqStatistics finds a common minimum set of channels and then apply
>> statistics on it. So do I need to average layout files for the
>> subject
>> group or is there any other way?
>>
>> Any help is much appreciated.
>>
>> Regards,
>> Manish
>>
>> ----------------------------------
>> 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.