<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>
                            fieldtrip mailing list<br>
                            <a href="mailto:fieldtrip@donders.ru.nl" target="_blank">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>
                    </div>
                    <pre><fieldset></fieldset>
_______________________________________________
fieldtrip mailing list
<a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></pre>
                  </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>
            fieldtrip mailing list<br>
            <a href="mailto:fieldtrip@donders.ru.nl" target="_blank">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>
      <pre><fieldset></fieldset>
_______________________________________________
fieldtrip mailing list
<a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></pre>
    </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>