Clusterplot not highlighting clusters & average layout file

[Ingrid Nieuwenhuis]

Dear Manish,

(I reply to the list again, than everyone can benefit).
That depends on what you want to test. If you have multiple frequencies in
your freq-data, and you just call freqanalysis, and you do not average over
specific frequency range, then clusterplot will look for clusters in the
time-frequency-place domain. This does not always make sense, for instance
in the lower frequencies we know that there are different frequency bands
that behave totally different (theta and alpha for instance). Then you can
better run freqanalysis for these frequencies separately (choose only 10Hz
for alpha, or choose 8:12 Hz and cfg.avgoverfreq = 'yes'). In this case you
can use clusterplot to visualize. 

If you have no idea which frequencies behave the same, or that is something
you are actually interested in (for instance you have a broadbanded high
gamma in your TFR) you can put freq-data with multiple frequencies in
freqanalysis and look at the cluster that comes out. This is a valid thing
to do, but you can only not use clusterplot to visualize then. What you can
do is plot with multiplotTFR with mask settings (cfg.zparam = 'stat',
cfg.maskparam = 'mask').

Best Ingrid

> -----Original Message-----
> From: Manish Saggar [mailto:manish.saggar at gmail.com]
> Sent: Monday, June 29, 2009 7:49 PM
> To: ingrid.nieuwenhuis at donders.ru.nl
> Subject: Re: [FIELDTRIP] Clusterplot not highlighting clusters & average
> layout file
> 
> Dear Ingrid,
> 
> Thanks for your reply. Sorry I was out and didn't get a chance to reply
> back.
> 
> Last question regarding your reply, can I simply run freqstats and
> clusterplot for each frequency separately?
> 
> Regards,
> Manish
> 
> On Fri, May 22, 2009 at 9:39 AM, Ingrid
> Nieuwenhuis<ingrid.nieuwenhuis at donders.ru.nl> wrote:
> > Dear Manish,
> >
> > If I understand correctly you have multiple frequencies over which you
> > cluster. Is that correct? (so cfg.avgoverfreq = 'no' when you called
> > freqstatistics?) In that case you should not call clusterplot because
> for
> > different frequencies there can be different channels part of the
> cluster.
> > Instead you can call multiplotER or multiplotTFR and use
> cfg.maskparameter =
> > 'mask' to plot the significant cluster.
> >
> > Hope this helps,
> > Ingrid
> >
> >
> >> -----Original Message-----
> >> From: Manish Saggar [mailto:manish.saggar at gmail.com]
> >> Sent: Friday, May 15, 2009 8:26 AM
> >> To: ingrid.nieuwenhuis at donders.ru.nl
> >> Cc: FIELDTRIP at NIC.SURFNET.NL
> >> Subject: Re: [FIELDTRIP] Clusterplot not highlighting clusters &
> average
> >> layout file
> >>
> >> 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.