[FieldTrip] cluster>nothing to plot

[Stephen Politzer-Ahles]

Hi Zita,

I think Lilla's explanation for why your clusters are not showing up in the
plot is right. If you're using the sample script from the cluster tutorial
on the wiki, you can probably resolve this problem by just plotting smaller
time windows; for example, to divide your epoch into 40 time windows instead
of 20, make the "timestep" half as big, make the loop run from k=1:40
instead of k=1:20, and edit the adjust the number of subplots accordingly.

Or, to get a more specific idea of the topography and time course of your
significant cluster(s), you can look in the variables
stat.posclusterslabelmat and stat.negclusterslabelmat, which tell you which
(time, channel) samples belong to significant clusters. (I find it easiest
to do this by writing those variables into Excel files and using Excel
functions to find where the significant clusters are, but it can be done in
Matlab as well.) This is a more exact way to see when and where significant
clusters appear, without worrying about what time windows to select for
plotting.

Best,
Steve


Message: 4
> Date: Fri, 7 Oct 2011 14:26:39 +0100
> From: Zita Eva Patai <eva.patai at psy.ox.ac.uk>
> To: Email discussion list for the FieldTrip project
>        <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] cluster>nothing to plot
> Message-ID:
>        <CACPtmWM5yqj7y2MhVGOP6YOh5nAWmJow=FCKcvbGUkntNibNtw at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you Stephen & Lilla!
>
> I think I am just a bit overwhelmed with my data...and I was hoping to get
> straightforward results for my epoch...
>
>
> On Fri, Oct 7, 2011 at 2:08 PM, Magyari, Lilla <Lilla.Magyari at mpi.nl>
> wrote:
>
> > hi Zita,
> >
> > I do not know what kind of script you wrote, therefore, it is difficult
> to
> > figure out what the problem is exactly. But your problems reminds me to
> the
> > following:
> > if you followed the FT tutorial for plotting the clusters, you must be
> > aware that it will plot only those channels in each time-bin that are
> part
> > of the cluster during the entire time-bin. So, if you use a 50 ms bin,
> and a
> > channel is part of the significant cluster only for 10 ms, you won't see
> > that channel on the plot. I hope this helps.
> >
> > Best,
> > Lilla
> >
> >
> > Zita Eva Patai wrote:
> >
> >> Sorry, I know the answer now, but I have another , similar problem:
> >>
> >> When i get the clusterplot figure (after i run the cluster analysis), it
> >> has the timebins every 4ms (bc i have a 250Hz sampling rate) with the
> >> significant clusters plotted. For a simplified plotting, i was trying to
> use
> >> the bit of script where i can specify the timesteps i want the clusters
> to
> >> be shown in (ex: every 50ms)
> >> But, depending on what timestep i use, sometimes it does not display the
> >> clusters that are significant, almost like if the period is not long
> enough,
> >> it will not show the clusters...
> >>
> >> Any ideas ?
> >>
> >> Thank you!
> >>
> >> On Fri, Oct 7, 2011 at 10:18 AM, Zita Eva Patai <eva.patai at psy.ox.ac.uk
> <mailto:
> >> eva.patai at psy.ox.ac.uk**>> wrote:
> >>
> >>    Dear All
> >>
> >>    I am running the Cluster-based permutation tests on event related
> >>    fields, and for the same dataset, with all settings identical, when
> >>    i run:
> >>    0-200ms: i get one significant cluster
> >>    but:
> >>    0-500ms: no significant clusters
> >>
> >>    why does my significant cluster disappear depending on the time
> >>    window i use?
> >>
> >>    thank you!
> >>    z
> >>
> >>
> >>    --
> >>    Zita Patai
> >>    DPhil Candidate, Experimental Psychology
> >>    University of Oxford
> >>    bcl.psy.ox.ac.uk/people/zita-**eva-patai/<
> http://bcl.psy.ox.ac.uk/people/zita-eva-patai/>
> >>    <http://bcl.psy.ox.ac.uk/**people/zita-eva-patai/<
> http://bcl.psy.ox.ac.uk/people/zita-eva-patai/>
> >> >
> >>    eva.patai at psy.ox.ac.uk <mailto:eva.patai at psy.ox.ac.uk**>
> >>
> >>
> >>
> >>
> >>
> >>
> >> --
> >>
> >> Zita Patai
> >> DPhil Candidate, Experimental Psychology
> >> University of Oxford
> >> bcl.psy.ox.ac.uk/people/zita-**eva-patai/<
> http://bcl.psy.ox.ac.uk/people/zita-eva-patai/><
> >> http://bcl.psy.ox.ac.uk/**people/zita-eva-patai/<
> http://bcl.psy.ox.ac.uk/people/zita-eva-patai/>
> >> >
> >> eva.patai at psy.ox.ac.uk <mailto:eva.patai at psy.ox.ac.uk**>
> >>
> >>
> >>
> >> ------------------------------**------------------------------**
> >> ------------
> >>
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> >>
> >
> > --
> > PhD student
> > Language and Cognition Group
> > research assistant
> > Neurobiology of Language Group
> >
> > Max Planck Institute for Psycholinguistics
> > Nijmegen, P.O. Box 310, 6500AH, the Netherlands
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> >
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>
>
>
> --
>
> Zita Patai
> DPhil Candidate, Experimental Psychology
> University of Oxford
> bcl.psy.ox.ac.uk/people/zita-eva-patai/
> eva.patai at psy.ox.ac.uk
>
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