<div dir="ltr">I checked it again, I used a data structure 'D1st' which included 90 trials.<br>I ran the following script and the result was a 'pre' structure. field pre.cov was a 90*248*248 matrix, i.e., the covariance was estimated for all the trials.<br>
<br>cfg = [];<br>cfg.covariance = 'yes';<br>cfg.removemean = 'no';<br>cfg.covariancewindow = [-0.1 0];<br>cfg.channel='MEG';<br>cfg.keeptrials = 'yes' ;<br>pre=ft_timelockanalysis(cfg, D1st);<br>
<br>you may find this script repository useful for LCMV analysis. it includes an older version of fieldtrip but this is the one we work with.<br><a href="http://yuval-harpaz.github.com/ft_BIU/">http://yuval-harpaz.github.com/ft_BIU/</a><br>
check the actual repository here (read the README) : <a href="https://github.com/yuval-harpaz/ft_BIU">https://github.com/yuval-harpaz/ft_BIU</a><br>good luck there, yuval.<br><br><div class="gmail_quote">On 23 March 2011 10:42, Jean-Michel Badier <span dir="ltr"><<a href="mailto:jean-michel.badier@univmed.fr">jean-michel.badier@univmed.fr</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff">
Thanks Yuval,<br>
<br>
<br>
Le 22/03/11 10:55, Yuval Harpaz a écrit :
<div class="im"><blockquote type="cite">
<div dir="ltr">So just run the commands on an unaveraged dataset.<br>
<br>
</div>
</blockquote></div>
Yes but that would be correct if there was only one trial in the
data set (see the message from Luisa).<div class="im"><br>
<br>
<blockquote type="cite">
<div dir="ltr">Another option to consider is the one used by Dr.
Robinson when performing SAMerf (we have his tool <a href="http://yuval-harpaz.github.com/SAM_BIU/" target="_blank">here</a>, works
for our 4D machine).<br>
</div>
</blockquote>
<br></div>
Thanks for it I will test it.<div><div></div><div class="h5"><br>
<blockquote type="cite">
<div dir="ltr">
The idea is to calculate the covariance on all trials, calculate
weights by this covariance (keep filter in LCMV) and then apply
these weights on the averaged data. I found it useful because
the covariance is better for longer datasets, and the averaging
in the end increases the signal to noise ratio. I do not know
exactly how to do it in fieldtrip.<br>
<br>
<div class="gmail_quote">On 22 March 2011 10:43, Jean-Michel
Badier <span dir="ltr"><<a href="mailto:jean-michel.badier@univmed.fr" target="_blank">jean-michel.badier@univmed.fr</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"> Dear Yuval,<br>
<br>
I have to admit that I did not look at the matlab
routines.<br>
In item 2 I suppose that the covariance is calculated for
each trial then averaged. In item 3 I would like to
calculate the covariance from all the signal (the trials
being concatenated).<br>
<br>
Jean-Michel<br>
<br>
Le 22/03/11 05:47, Yuval Harpaz a écrit :
<div>
<div>
<blockquote type="cite">
<div dir="ltr">Dear Jean Michel
<div>As far as I know you can do it on an averaged
data structure (item 1) or do the same with the
data structure before averaging (3). I did not
understand what you meant by 2. </div>
<div><br>
</div>
<div>Yuval<br>
<br>
<div class="gmail_quote">On 21 March 2011 22:58,
Jean-Michel Badier <span dir="ltr"><<a href="mailto:jean-michel.badier@univmed.fr" target="_blank">jean-michel.badier@univmed.fr</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"> Dear
fieldtrip users,<br>
<br>
There are different ways of estimating the
covariance for LCMV calculation.<br>
If I am correct: <br>
<br>
1. As suggested in one of the tutorial one
can apply the calculation of the
covariance directly on the average data
(for the different periods of interest
that are at least a base line and the
period of interest).<br>
<br>
2. Estimate the covariance from the
average of the covariance rather than the
covariance of the average using
cfg.keeptrials = "yes"<br>
<br>
3. Estimate the covariance from the whole
trials concatenated together. <br>
Is there an easy way to do that in
fieldtrip (beside create a new data set of
one trial constituted of all the trials)?<br>
<br>
Thanks<br>
<br>
Jean-Michel<br>
<br>
<div>
<address>-- </address>
<address style="margin-bottom: 0cm;">Jean-Michel
Badier PhD</address>
<address style="margin-bottom: 0cm;"><br>
</address>
<address style="margin-bottom: 0cm;" align="LEFT"><font color="#000000"><font face="Times Roman, serif"><font size="3">Laboratoire de
MagnétoEncéphaloGraphie</font></font></font></address>
<address style="margin-bottom: 0cm;" align="LEFT"><font color="#000000"><font face="Times Roman, serif"><font size="3">INSERM U751. Aix
Marseille Université</font></font></font></address>
<address style="margin-bottom: 0cm;" align="LEFT"><font color="#000000"><font face="Times Roman, serif"><font size="3">33 (0)4 91 38 55 62 </font></font></font></address>
<address style="margin-bottom: 0cm;" align="LEFT"><a href="mailto:jean-michel.badier@univmed.fr" target="_blank"><font color="#000af1"><font face="Times
Roman, serif"><font size="3"><u>jean-michel.badier@univmed.fr</u></font></font></font></a></address>
<address style="margin-bottom: 0cm;" align="LEFT"><br>
</address>
<address style="margin-bottom: 0cm;" align="LEFT"><font color="#000000"><font face="Times Roman, serif"><font size="2"><font color="#000000"><font face="Times Roman, serif"><font size="2">Service de
Neurophysiologie Clinique.
</font></font></font>CHU
Timone</font></font></font></address>
<address style="margin-bottom: 0cm;" align="LEFT"><font color="#000000"><font face="Times Roman, serif"><font size="2">264 Rue
Saint-Pierre, 13005
Marseille-France</font></font></font></address>
<address style="margin-bottom: 0cm;" align="LEFT"><br>
</address>
<p style="margin-bottom: 0cm;"><br>
</p>
</div>
</div>
<br>
_______________________________________________<br>
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</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
<div dir="ltr">Y.Harpaz<br>
<br>
a link to the BIU MEG lab:<br>
<a href="http://faculty.biu.ac.il/%7Egoldsa/index.html" target="_blank">http://faculty.biu.ac.il/~goldsa/index.html</a>
<div>
<div><br>
</div>
<div> " Why, Dan," ask the people in
Artificial Intelligence, "do you waste
your time conferring with those
neuroscientists? They wave their hands
about information processing and worry
about where it happens, and
which neurotransmitters are involved, and
all those boring facts, but they haven't a
clue about the computational requirements
of higher cognitive functions." "Why,"
ask the neuroscientists, "do you waste
your time on the fantasies of Artificial
Intelligence? They just invent
whatever machinery they want, and say
unpardonably ignorant things about the
brain." The cognitive psychologists,
meanwhile, are accused of concocting
models with neither biological
plausibility nor proven computational
powers; the anthropologists wouldn't know
a model if they saw one, and the
philosophers, as we all know, just take in
each other's laundry, warning about
confusions they themselves have created,
in an arena bereft of both data and
empirically testable theories. With
so many idiots working on the problem, no
wonder consciousness is still a mystery.<i>
Philosopher Daniel Dennet, consciousness
explained, pp. 225</i></div>
</div>
</div>
<br>
</div>
</div>
<pre><fieldset></fieldset>
_______________________________________________
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</blockquote>
<br>
<div>
<p style="margin-bottom: 0cm;" align="LEFT"><br>
</p>
<p style="margin-bottom: 0cm;"><br>
</p>
</div>
</div>
</div>
</div>
<br>
_______________________________________________<br>
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<a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><br>
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</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
<div dir="ltr">Y.Harpaz<br>
<br>
a link to the BIU MEG lab:<br>
<a href="http://faculty.biu.ac.il/%7Egoldsa/index.html" target="_blank">http://faculty.biu.ac.il/~goldsa/index.html</a>
<div>
<div><br>
</div>
<div> " Why, Dan," ask the people in Artificial
Intelligence, "do you waste your time conferring with
those neuroscientists? They wave their hands about
information processing and worry about where it happens,
and which neurotransmitters are involved, and all those
boring facts, but they haven't a clue about the
computational requirements of higher cognitive functions."
"Why," ask the neuroscientists, "do you waste your
time on the fantasies of Artificial Intelligence? They
just invent whatever machinery they want, and say
unpardonably ignorant things about the brain." The
cognitive psychologists, meanwhile, are accused
of concocting models with neither biological plausibility
nor proven computational powers; the anthropologists
wouldn't know a model if they saw one, and the
philosophers, as we all know, just take in each
other's laundry, warning about confusions they themselves
have created, in an arena bereft of both data and
empirically testable theories. With so many idiots working
on the problem, no wonder consciousness is still a
mystery.<i> Philosopher Daniel Dennet, consciousness
explained, pp. 225</i></div>
</div>
</div>
<br>
</div>
<pre><fieldset></fieldset>
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fieldtrip mailing list
<a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a>
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</blockquote>
<br>
<br>
</div></div><div>-- <br><font color="#888888">
<p style="margin-bottom: 0cm;">Jean-Michel Badier</p></font><div class="im">
<p style="margin-bottom: 0cm;"><br>
</p>
<p style="margin-bottom: 0cm;" align="LEFT"><font color="#000000"><font face="Times Roman, serif"><font size="3">Laboratoire
de MagnétoEncéphaloGraphie</font></font></font></p>
<p style="margin-bottom: 0cm;" align="LEFT"><font color="#000000"><font face="Times Roman, serif"><font size="3">INSERM
U751. Aix Marseille Université</font></font></font></p>
<p style="margin-bottom: 0cm;" align="LEFT"><font color="#000000"><font face="Times Roman, serif"><font size="3">33
(0)4 91 38 55 62 </font></font></font></p>
<p style="margin-bottom: 0cm;" align="LEFT"><a href="mailto:jean-michel.badier@univmed.fr" target="_blank"><font color="#000af1"><font face="Times Roman, serif"><font size="3"><u>jean-michel.badier@univmed.fr</u></font></font></font></a></p>
<p style="margin-bottom: 0cm;" align="LEFT"><br>
</p>
<p style="margin-bottom: 0cm;" align="LEFT"><font color="#000000"><font face="Times Roman, serif"><font size="2"><font color="#000000"><font face="Times Roman, serif"><font size="2">Service
de Neurophysiologie Clinique. </font></font></font>CHU
Timone</font></font></font></p>
<p style="margin-bottom: 0cm;" align="LEFT"><font color="#000000"><font face="Times Roman, serif"><font size="2">264
Rue Saint-Pierre, 13005 Marseille-France</font></font></font></p>
<p style="margin-bottom: 0cm;" align="LEFT"><br>
</p>
<p style="margin-bottom: 0cm;"><br>
</p>
</div></div>
</div>
<br>_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br></blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr">Y.Harpaz<br>
<br>a link to the BIU MEG lab:<br><a href="http://faculty.biu.ac.il/%7Egoldsa/index.html" target="_blank">http://faculty.biu.ac.il/~goldsa/index.html</a><div><div><br></div><div> " Why, Dan," ask the people in Artificial Intelligence, "do you waste your time conferring with those neuroscientists? They wave their hands about information processing and worry about where it happens, and which neurotransmitters are involved, and all those boring facts, but they haven't a clue about the computational requirements of higher cognitive functions." "Why," ask the neuroscientists, "do you waste your time on the fantasies of Artificial Intelligence? They just invent whatever machinery they want, and say unpardonably ignorant things about the brain." The cognitive psychologists, meanwhile, are accused of concocting models with neither biological plausibility nor proven computational powers; the anthropologists wouldn't know a model if they saw one, and the philosophers, as we all know, just take in each other's laundry, warning about confusions they themselves have created, in an arena bereft of both data and empirically testable theories. With so many idiots working on the problem, no wonder consciousness is still a mystery.<i> Philosopher Daniel Dennet, consciousness explained, pp. 225</i></div>
</div></div><br>
</div>