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Hello Tyler,<br>
<br>
okay, I'd say the script should run like this (regarding channel
selection). Maybe it's really the data then. If you keep getting
errors, you can send me those as well.<br>
<br>
Regarding the number of data points: The error you are getting
depends on a number of parameters TEprepare uses to determine the
optimal embedding dimension and embedding delay. TEprepare checks
whether you have enough samples in one trial after taking into
account the ACT, cfg.actthrvalue, cfg.ragdim, cfg.ragtau and the
assumed interaction delay (these parameters determine the maximum
possible length, i.e. the worst case, of your embedding).<br>
<br>
Could you tell me the sampling rate of your data? If your data was
sampled at 1000Hz, 3/9th of 500 ms should give you about 167 sample
points for cfg.repPred, which would be okay. <br>
<br>
Otherwise, you may alter the parameters mentioned above, e.g. you
can check whether you could lower the actthrvalue. The actthrvalue
is used to exclude all trials with an ACT higher than the threshold.
The value you put in there should be based on the filtering of the
data prior to TE analysis (e.g. if you highpass filter your data at
10 Hz and have a sampling rate of 1000Hz, you shouldn't find any
autocorrelation above 100 samples. In that case, you may use 100 as
a threshold).<br>
<br>
What values do you enter for the other parameters (assumed
interaction delay u, specified in
cfg.predicttimemin_u/cfg.predicttimemax_u, embedding parameters to
be scanned in cfg.ragdim and cfg.ragtau)? Maybe you can adjust those
as well, to be able to enter a higher value for .repPred.<br>
<br>
Best, Patricia<br>
<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 04/11/2014 12:44 PM, Tyler Grummett
wrote:<br>
</div>
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<p style="">Hello Patricia,<br>
</p>
<p style=""><br>
</p>
<p style="">I have previously selected the channels that are
EEG, I am not entering in 'EEG' or anything.<br>
</p>
<p style=""><br>
</p>
<div> cfgTEP = [];</div>
<div> cfgTEP.Path2TSTOOL = fullfile(
matlabrootpath, 'Matlab', 'OpenTSTOOL'); % dont add this to
matlab path</div>
<div> cfgTEP.toi = [ min( [vchan.time{ :}]), max(
[vchan.time{ :}])];</div>
<div style=""><span style="font-size: 12pt;">
cfgTEP.channel = vchan.label( comps);</span><span
style="font-size: 12pt;"></span><br>
</div>
<p style=""><br>
</p>
<p style="">After playing around with it for a bit I dont
think it is the channel combinations, but the data.<br>
</p>
<p style=""><br>
</p>
<p style="">If I can ask a separate question, what is an
optimal length for the trials? My trials are about 500 ms
long and it gives me the following error:<br>
</p>
<p style=""><br>
</p>
<div>Error using TEprepare (line 710)</div>
<div>TRENTOOL ERROR: Not enough points in timeseries for
current analysis settings: cfg.repPred too big, or</div>
<div style="">max(cfg.ragdim)*max(cfg.ragtaurange) too big, or
maximum u to big<br>
</div>
<div style=""><br>
</div>
<div style="">It is recommended that the cfgTEP.repPred is
size(data.trial{1,1},2)*(3/4)<br>
</div>
<div style=""><br>
</div>
<div style="">However it only works for me if it is <span
style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 16px; background-color: rgb(255, 255, 255);">size(data.trial{1,1},2)*(3/9)</span>
.<br>
</div>
<div style=""><br>
</div>
<div style="">Then it runs fine, but Im worried about changing
this.<br>
</div>
<div style=""><br>
</div>
<div style="">Tyler<br>
</div>
<p style=""><br>
</p>
<p style=""><br>
</p>
<div>
<div name="divtagdefaultwrapper"
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:; margin:0">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-size:13px">*************************
<div style="font-family:Tahoma"><br>
</div>
<div><font face="Arial"><i>Tyler Grummett ( BBSc,
BSc(Hons I))</i></font></div>
<div><font face="Arial"><i>PhD Candidate</i></font></div>
<div><font face="Arial"><i>Brain Signals
Laboratory</i></font></div>
<div><font face="Arial"><i>Flinders University</i></font></div>
<div><font face="Arial"><i>Rm 5A301</i></font></div>
<div><font face="Arial"><i>Ext 66124</i></font></div>
</div>
</div>
</div>
</div>
</div>
</div>
<div style="color:rgb(40,40,40)">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font
style="font-size:11pt" color="#000000" face="Calibri,
sans-serif"><b>From:</b> <a
class="moz-txt-link-abbreviated"
href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>
<a class="moz-txt-link-rfc2396E"
href="mailto:fieldtrip-bounces@science.ru.nl"><fieldtrip-bounces@science.ru.nl></a>
on behalf of Patricia Wollstadt <a
class="moz-txt-link-rfc2396E"
href="mailto:Patricia.Wollstadt@gmx.de"><Patricia.Wollstadt@gmx.de></a><br>
<b>Sent:</b> Friday, 11 April 2014 6:42 PM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] TRENTOOL bad channel
combinations</font>
<div> </div>
</div>
<div>Hello Tyler,<br>
<br>
TRENTOOL does not support the exclusion of channels like
FieldTrip does (e.g. {'all', '-MLx', '-EOG'}), you have
to explicitly specify channels OR combinations of channels
for analysis in the cfg structure passed to TEprepare:<br>
<br>
% cfg.sgncmb = list of channelpairs cell array
(Nx(source, target))<br>
% or<br>
% cfg.channel = list of channels cell array - testing
will be done all-by-all<br>
<br>
If you provide a list of channel combinations in
cfg.sgncmb, TRENTOOL will analyze these combinations only;
if you provide a list of channels in cfg.channel,
TEprepare will build all possible channel combinations
from the list and TRENTOOL will analyze these
combinations. (Also, channel names have to match the
channel labels in data.label.)<br>
<br>
So, a way to exclude bad channel combinations would be to
provide a list of all channels that should be included in
the analysis in cfg.channel and let TEprepare build the
channel combinations from that. <br>
<br>
I hope this answers your question. Please let me know if
you encounter any more problems.<br>
<br>
Best, <br>
Patricia<br>
<br>
<br>
<br>
On 04/11/2014 04:38 AM, Tyler Grummett wrote:<br>
<blockquote type="cite">
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<div style="font-size:12pt; color:#000000;
background-color:#FFFFFF;
font-family:Calibri,Arial,Helvetica,sans-serif">
<p style="">Hello fieldtrip,<br>
</p>
<p style=""><br>
</p>
<p style="">Has anyone worked out how to handle bad
channel combinations in TRENTOOL using TEprepare?<br>
</p>
<p style=""><br>
</p>
<p style="">In my experience it just crashes. I am
hoping for a way to calculate the bad channel
combinations before running TEprepare.<br>
</p>
<p style=""><br>
</p>
<p style="">If anyone can help, that will be greatly
appreciated!!<br>
</p>
<p style=""><br>
</p>
<p style="">Tyler<br>
</p>
<div>
<p><br>
</p>
<div name="divtagdefaultwrapper"
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:; margin:0">
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<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma;
font-size:13px">
<div style="font-size:13px">*************************
<div style="font-family:Tahoma"><br>
</div>
<div><font face="Arial"><i>Tyler Grummett
( BBSc, BSc(Hons I))</i></font></div>
<div><font face="Arial"><i>PhD Candidate</i></font></div>
<div><font face="Arial"><i>Brain Signals
Laboratory</i></font></div>
<div><font face="Arial"><i>Flinders
University</i></font></div>
<div><font face="Arial"><i>Rm 5A301</i></font></div>
<div><font face="Arial"><i>Ext 66124</i></font></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre>_______________________________________________
fieldtrip mailing list
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<address><font color="#666666"><small><font
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<br>
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<address><font color="#666666"><small><font
face="Helvetica, Arial, sans-serif">Patricia
Wollstadt, PhD Student<br>
<br>
</font></small></font></address>
<address><font color="#666666"><small><font
face="Helvetica, Arial, sans-serif">MEG Unit,
Brain Imaging Center</font></small></font></address>
<address><font color="#666666"><small><font
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<br>
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<pre wrap="">_______________________________________________
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http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</pre>
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<address><font color="#666666"><small><font face="Helvetica,
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<address><font color="#666666"><small><font face="Helvetica,
Arial, sans-serif">Patricia Wollstadt, PhD Student<br>
<br>
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<address><font color="#666666"><small> </small></font></address>
<address><font color="#666666"><small><font face="Helvetica,
Arial, sans-serif"> MEG Unit, Brain Imaging Center</font></small></font></address>
<address><font color="#666666"><small><font face="Helvetica,
Arial, sans-serif"> Goethe University, Frankfurt, Germany<br>
<br>
</font></small></font></address>
<address><font color="#666666"><small><font face="Helvetica,
Arial, sans-serif">Heinrich Hoffmann Strasse 10, Haus 93 B</font></small></font></address>
<address><font color="#666666"><small><font face="Helvetica,
Arial, sans-serif">D - 60528 Frankfurt am Main</font></small></font></address>
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