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    Hi all,<br>
    <br>
    A follow up on this and some new issues:<br>
    <br>
    1) I first tried Jörn's approach by creating my own BEM, always fun
    to make it yourself ;) However, I did not succeed since:<br>
    a) the dipoli method does not work on Windows<br>
    b) I downloaded the openmeeg toolbox, but got an error
    "om_minverser.exe has stopped working" I've emailed their buglist<br>
    c) bemcp did run, but the result was not ok (see attachement). I
    also got the warning "% Warning: Matrix is singular, close to
    singular or badly scaled. Results may be inaccurate." several times,
    so that might be the problem.<br>
    d) and asa gave the following error: % Error using
    ft_prepare_headmodel (line 201) % You must supply a valid
    cfg.hdmfile for use with ASA headmodel<br>
    <br>
    And away went my determination to do it myself, so I continued using
    the<a
href="http://fieldtrip.fcdonders.nl/template/headmodel?s[]=standard&s[]=bem">
      standard_bem.mat</a>. (I did not know this existed, I've added
    this link to note in the <a
href="http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg?&#background">headmodel
      tutorial</a> to make it easier to find, thanks Tzvetan for
    pointing this out!).<br>
    <br>
    2) This worked and after some fiddling to get the electrodes aligned
    it looks okay (see attached). <br>
    However, as you can see in the figures, I have several very low
    electrodes, that are lower than the skin mesh. So I was wondering if
    this is a problem? Since for accurate calculation of how the
    currents flow from these low electrodes, I assume one needs the skin
    to go till there? What happens when I have electrodes floating in
    thin air? <br>
    <b>So my question is:</b><br>
    a) will this cause great inaccuracies?<br>
    b) if so, how can I extend the skin to go lower? The template MRI
    only goes that far to the bottom... Trick anyone?<br>
    <br>
    Thanks again,<br>
    Ingrid<br>
    <br>
    <br>
    <div class="moz-cite-prefix">On 4/9/2013 9:39 AM, Ingrid Nieuwenhuis
      wrote:<br>
    </div>
    <blockquote cite="mid:5164443E.5040909@berkeley.edu" type="cite">
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      Thanks Jörn and Tzvetan for the scripts! I'll try it out and put
      it on the wiki.<br>
      Have a great day,<br>
      Ingrid<br>
      <br>
      <div class="moz-cite-prefix">On 4/9/2013 12:32 AM, Tzvetan Popov
        wrote:<br>
      </div>
      <blockquote
        cite="mid:43CC12AA-D78E-4374-A201-FD4F7B2C8736@uni-konstanz.de"
        type="cite">
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        Dear Ingrid,
        <div><br>
        </div>
        <div>in addition to Jorn's approach since you don't have MR and
          digitized elec position's you can load and realign the
          electrodes to the standard bem. Subsequently you can calculate
          the lead field and  continue with your analysis pipeline.</div>
        <div>Good luck</div>
        <div>tzvetan</div>
        <div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            color: rgb(37, 153, 45); ">%% read electrodes</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            color: rgb(178, 69, 243); "><span style="color: #000000">elec

              = ft_read_sens(</span>'/your
            path/fieldtrip-20130324/template/electrode/GSN-HydroCel-128.sfp'<span
              style="color: #000000">);</span></div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            color: rgb(37, 153, 45); ">%% read  headmodel</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            color: rgb(178, 69, 243); "><span style="color: #000000">templateheadmodel

              = </span>'/your
            path/fieldtrip-20130324/template/headmodel/standard_bem.mat'<span
              style="color: #000000">;</span></div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            ">load(templateheadmodel);</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            color: rgb(37, 153, 45); ">%% electrode realign as good as
            possible</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            color: rgb(37, 153, 45); ">% i.e. translate 0 -2 1.5</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            ">cfg=[];</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            ">cfg.method = <span style="color: #b245f3">'interactive'</span>;</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            ">cfg.elec = elec;</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            ">cfg.headshape = vol.bnd(1).pnt;</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            ">elecR = ft_electroderealign(cfg);</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            color: rgb(37, 153, 45); ">%% verify how the electrodes fit
            toghether with the brain volume</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            ">cfg=[];</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            ">cfg.method = <span style="color: #b245f3">'interactive'</span>;</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            ">cfg.elec = elecR;</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            ">cfg.headshape = vol.bnd(3).pnt;</div>
          <div style="margin: 0px; font-size: 9px; font-family: Courier;
            ">elecR = ft_electroderealign(cfg);</div>
        </div>
        <div><br>
        </div>
        <div>
          <div><br class="Apple-interchange-newline">
            <blockquote type="cite">
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                <div class="moz-cite-prefix">Hi Ingrid,<br>
                  <br>
                  I just happen to done this a few weeks back, I changed
                  things in the meanwhile, but I hope that the below
                  steps are complete:<br>
                  <i><small>% read in the template MRI<br>
                          if isunix<br>
                            mri =
ft_read_mri('/home/common/matlab/fieldtrip/external/spm8/templates/T1.nii');<br>
                          elseif ispc<br>
                            mri = ft_read_mri(fullfile('M:',
                      'FieldTrip', 'trunk', 'external', 'spm8',
                      'templates', 'T1.nii'));<br>
                          end<br>
                      <br>
                      <br>
                      % segment the MRI<br>
                      cfg           = [];<br>
                      cfg.output    = {'brain'  'skull'  'scalp'};<br>
                      segmentedmri  = ft_volumesegment(cfg, mris);<br>
                      <br>
                      <br>
                      % create the headmodel (BEM)<br>
                      cfg        = [];<br>
                      %cfg.method ='openmeeg'; % TODO FIXME download
                      openmeeg<br>
                      if isunix<br>
                        cfg.method ='dipoli'; % dipoli only works under
                      linux<br>
                      else<br>
                        disp('TODO FIXME stick to dipoli for now or
                      download openmeeg\n');<br>
                        keyboard;<br>
                      end<br>
                      hdm        = ft_prepare_headmodel(cfg,
                      segmentedmri);<br>
                      <br>
                      elec       = ft_read_sens('standard_1020.elc');<br>
                      hdm        = ft_convert_units(hdm, elec.unit);<br>
                      <br>
                        cfg = [];<br>
                        cfg.grid.xgrid  = -125:8:125; <br>
                        cfg.grid.ygrid  = -125:8:125; <br>
                        cfg.grid.zgrid  = -125:8:125;<br>
                        cfg.grid.tight  = 'yes'; <br>
                        cfg.grid.unit   = hdm.unit;<br>
                        cfg.inwardshift = -1.5;<br>
                        cfg.vol        = hdm;<br>
                        grid  = ft_prepare_sourcemodel(cfg)<br>
                        grid        = ft_convert_units(grid, elec.unit);<br>
                      <br>
                      figure;<br>
                      hold on;<br>
                      ft_plot_mesh(hdm.bnd(1), 'facecolor',[0.2 0.2
                      0.2], 'facealpha', 0.3, 'edgecolor', [1 1 1],
                      'edgealpha', 0.05);<br>
                      ft_plot_mesh(grid.pos(grid.inside, :));<br>
                      <br>
                      % this step is not necessary, cause you will see
                      that everything is already aligned<br>
                        cfg           = [];<br>
                        cfg.method    = 'interactive';<br>
                        cfg.elec      = elec;<br>
                        cfg.headshape = hdm.bnd(1);<br>
                        tmp  = ft_electroderealign(cfg);<br>
                        elec = tmp; % I had a bug here that I couldn't
                      assign elec directly<br>
                      <br>
                      %% verify location of occipital electrodes<br>
                      <br>
                      occ_elec = elec;<br>
                      occ_chan = ft_channelselection({'O*', 'PO*',
                      'Cz*', 'Fz*'}, elec.label);<br>
                      occ_idx = match_str(elec.label, occ_chan);<br>
                      occ_elec.chanpos = occ_elec.chanpos(occ_idx, :);<br>
                      occ_elec.elecpos = occ_elec.elecpos(occ_idx, :);<br>
                      occ_elec.label = occ_elec.label(occ_idx, :);<br>
                      figure;<br>
                      ft_plot_sens(occ_elec)<br>
                      hold on;<br>
                      ft_plot_vol(ft_convert_units(hdm, elec.unit))</small></i><br>
                  <br>
                  <br>
                  Afair, that's all that is needed. Of course you need
                  to adjust folder and file names.<br>
                  <br>
                  Greetings<br>
                  Jörn<br>
                  <br>
                  On 4/9/2013 2:04 AM, Ingrid Nieuwenhuis wrote:<br>
                </div>
                <blockquote cite="mid:51635B04.7090004@berkeley.edu"
                  type="cite">Hi all, <br>
                  <br>
                  I'd like to do source analysis (loreta and or DICS) on
                  my EEG data. I don't have anatomical MRIs and I don't
                  have a measurement of the scalp surface. So I'd like
                  to use a template MRI or a template head model that is
                  located in the FieldTrip template directory. I have
                  EGI (128 channels) data and electrode positions (not
                  subject specific, just the standard file also
                  available in FieldTrip electrode template,
                  GSN-HydroCel-128.sfp), but I'm kind of stuck how to
                  start. I don't see any examples on the FieldTrip page
                  of how to make a headmodel and volume conduction model
                  giving only this limited data. I'd be happy to make it
                  into a example Matlab script on the FieldTrip page
                  after I got it to work. Would someone be able to give
                  me some pointers, or example code? <br>
                  <br>
                  Thanks a lot! <br>
                  Ingrid <br>
                  <br>
                </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
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: <a moz-do-not-send="true" 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 moz-do-not-send="true" 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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                href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></blockquote>
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                                  <div>*******************************************</div>
                                  <div>Tzvetan Popov  </div>
                                  <div>Clinical Psychology       </div>
                                  <div>University of Konstanz</div>
                                  <div>Box 23</div>
                                  <div>78457 Konstanz, GERMANY</div>
                                  <div>Phone: 0049-7531-883086</div>
                                  <div>Fax:      0049-7531-884601</div>
                                  <div>Email:  <a moz-do-not-send="true"
href="mailto:tzvetan.popov@uni-konstanz.de">tzvetan.popov@uni-konstanz.de</a></div>
                                </div>
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        <pre wrap="">_______________________________________________
fieldtrip mailing list
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>
<a moz-do-not-send="true" 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>
      <pre class="moz-signature" cols="72">-- 
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305 </pre>
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      <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>
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    <pre class="moz-signature" cols="72">-- 
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305 </pre>
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