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Hey Stephen,<br>
<br>
please check your FT path. You are definitely not using a recent FT
version, because the line you quoted on statistics_wrapper does not
exist anymore. You can verify your path by typing in Matlab 'which
ft_defaults' or 'which ft_timelockstatistics' (without the quotes).<br>
<br>
Due to recent changes, it might additionally help to read these two
FAQs:<br>
<a class="moz-txt-link-freetext" href="http://fieldtrip.fcdonders.nl/faq/how_can_i_define_neighbouring_sensors">http://fieldtrip.fcdonders.nl/faq/how_can_i_define_neighbouring_sensors</a><br>
<a class="moz-txt-link-freetext" href="http://fieldtrip.fcdonders.nl/faq/how_does_ft_neighbourselection_work">http://fieldtrip.fcdonders.nl/faq/how_does_ft_neighbourselection_work</a><br>
<br>
Anyway, the tutorial wiki page is indeed out of date, as the
neighbourselection is not included correctly anymore. I'm gonna fix
this :) The only thing which you need to add is
cfg.neighbours=ft_neighbourselection(cfg, [...]) before calling
ft_timelockstatistics. That's all that changed. <br>
<br>
Best regards,<br>
Jörn<br>
<br>
<br>
On 9/19/2011 4:43 PM, Stephen Politzer-Ahles wrote:
<blockquote
cite="mid:CAJT2k__fTwVsN28VtH6cWtnNf2c=SXztbz+unFeaV_mXBLgb+g@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div><span class="st">Jörn,<br>
<br>
Thanks lot for this information. I tried specifying
cfg.layout and got a new error message:<br>
<br>
??? Error using ==> ft_neighbourselection at 130<br>
Sensor distance is measured in an unknown unit type<br>
<br>
Error in ==> statistics_wrapper at 241<br>
cfg.neighbours = ft_neighbourselection(cfg,varargin{1});<br>
<br>
Error in ==> ft_timelockstatistics at 123<br>
[stat, cfg] = statistics_wrapper(cfg, varargin{:});<br>
<br>
<br>
(I get the same message when trying to run
neighbours=ft_neighbourselection(cfg,data) with that layout
file specified.) The layout file I was using is based
directly on EEG1010.lay which is included in fieldtrip, and
it works fine when I use it for topoplotting and
multiplotting, so I'm not sure why it's causing errors when
fed to ft_neighbourselection.<br>
<br>
As for the version, I actually am using the most recent
version (which I downloaded yesterday before trying to run
cluster statistics, and updated my path accordingly), but
still getting these errors. The code I've been trying to
run, though, is based on the sample code on the wiki page <a
moz-do-not-send="true"
href="http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock">http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock</a>,
which may be out of date.<br>
<br>
Is there perhaps anyone on the list who has run cluster
statistics on EEG data and would be willing to share a
sample of their code?<br>
<br>
Best,<br>
Steve<br>
<br>
</span> </div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Message: 1<br>
Date: Mon, 19 Sep 2011 09:12:32 +0200<br>
From: "J?rn M. Horschig" <<a moz-do-not-send="true"
href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>><br>
To: Email discussion list for the FieldTrip project<br>
<<a moz-do-not-send="true"
href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
Subject: Re: [FieldTrip] Problem with EEG channels in<br>
ft_neighborselection when running cluster statistics<br>
Message-ID: <<a moz-do-not-send="true"
href="mailto:4E76EB60.9080801@donders.ru.nl">4E76EB60.9080801@donders.ru.nl</a>><br>
Content-Type: text/plain; charset="iso-8859-1";
Format="flowed"<br>
<br>
Hey Stephen,<br>
<br>
You need to specify the position of your electrodes, which are
mostly<br>
stored in an 'elec' structure. If you do not have that
available, you<br>
can circumvent the problem by defining a cfg.layout. In that
case,<br>
neighbouring sensors will be selected according to how they
are placed<br>
in that layout-file you specify. That's not 100% correct of
course, but<br>
at least an estimate how the sensors are positioned (note that
a layout<br>
has only 2D coordinates). For example, you could use
cfg.layout =<br>
'EEG1010.lay' as a start.<br>
<br>
Anyway, could you try using a more recent version of
FieldTrip? A few<br>
months ago, we changed the way the neighbourselection works
(actually,<br>
you have to call cfg.neighbours = ft_neighbourselection
manually, now).<br>
You can then also check with cfg.feedback = 'yes' whether the<br>
neighbourselection looks alright to you (that's the same as
calling<br>
ft_neighbourplot)<br>
<br>
Hope it helps! Best regards,<br>
J?rn<br>
<br>
<br>
<br>
On 9/17/2011 6:42 PM, Stephen Politzer-Ahles wrote:<br>
> When attempting to run cluster statistics on my EEG data
(originally<br>
> from Neuroscan .CNT, then processed in EEGLAB and finally
imported to<br>
> fieldtrip) using ft_timelockstatistics(), I receive the
following<br>
> error message:<br>
><br>
> ??? Error using ==> ft_neighbourselection at 114<br>
> Did not find gradiometer or electrode information.<br>
><br>
> Error in ==> statistics_wrapper at 241<br>
> cfg.neighbours =
ft_neighbourselection(cfg,varargin{1});<br>
><br>
> Error in ==> ft_timelockstatistics at 123<br>
> [stat, cfg] = statistics_wrapper(cfg, varargin{:});<br>
><br>
> This seems to be because when I use cfg.channel =
{'EEG'}; with my<br>
> data, the channel information (the variable "sens" used
in<br>
> ft_neighbourselection) consists only of the list of
channel labels:<br>
><br>
> sens = {'FPZ' 'CPZ' 'FP2' 'F7' .........}<br>
><br>
> On the other hand, when I run timelockstatistics on the
sample data<br>
> from the wiki, "sens" includes much more information:<br>
><br>
> sens =<br>
><br>
> pnt: [151x3 double]<br>
> ori: [356x3 double]<br>
> tra: [184x356 double]<br>
> label: {151x1 cell}<br>
> unit: 'cm'<br>
><br>
> I think most of that extra information is planar gradient
data (i.e.,<br>
> it comes from GA_FIC.grad). Since my data are EEG data, I
assume it<br>
> wouldn't make sense to use ft_megplanar on them. So,
assuming that I<br>
> need to get the extra channel location information into
my EEG data,<br>
> does anyone have any ideas on how to do that?<br>
><br>
> Best,<br>
> Steve Politzer-Ahles<br>
><br>
> --<br>
> Stephen Politzer-Ahles<br>
> University of Kansas<br>
> Linguistics Department<br>
> <a moz-do-not-send="true"
href="http://www.linguistics.ku.edu/" target="_blank">http://www.linguistics.ku.edu/</a><br>
><br>
><br>
> _______________________________________________<br>
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> <a moz-do-not-send="true"
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> <a moz-do-not-send="true"
href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<br>
<br>
--<br>
J?rn M. Horschig<br>
PhD Student<br>
Donders Institute for Brain, Cognition and Behaviour<br>
Centre for Cognitive Neuroimaging<br>
Radboud University Nijmegen<br>
Neuronal Oscillations Group<br>
<br>
P.O. Box 9101<br>
NL-6500 HB Nijmegen<br>
The Netherlands<br>
<br>
Contact:<br>
E-Mail: <a moz-do-not-send="true"
href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a><br>
Tel: <a moz-do-not-send="true"
href="tel:%2B31-%280%2924-36-68493" value="+31243668493">+31-(0)24-36-68493</a><br>
Web: <a moz-do-not-send="true"
href="http://www.ru.nl/donders" target="_blank">http://www.ru.nl/donders</a><br>
<br>
Visiting address:<br>
Trigon, room 2.30<br>
Kapittelweg 29<br>
NL-6525 EN Nijmegen<br>
The Netherlands<br>
<br>
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</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Stephen Politzer-Ahles<br>
University of Kansas<br>
Linguistics Department<br>
<a moz-do-not-send="true" href="http://www.linguistics.ku.edu/">http://www.linguistics.ku.edu/</a><br>
<br>
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<br>
<pre wrap="">_______________________________________________
fieldtrip mailing list
<a class="moz-txt-link-abbreviated" href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>
<a class="moz-txt-link-freetext" href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands
Contact:
E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>
Tel: +31-(0)24-36-68493
Web: <a class="moz-txt-link-freetext" href="http://www.ru.nl/donders">http://www.ru.nl/donders</a>
Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands</pre>
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