<div>Hi Robert,</div>
<div> </div>
<div>Thanks very much for the clarifications.</div>
<div> </div>
<div>Quick question about the BEM model you supplied--is it correct to just pass in the vol structure contained in the standard_vol.mat along with an elec structure containing the nx3 array of electrode coordinates in MNI space? That is, is the following correct:
</div>
<div> </div>
<div>load standard_vol.mat</div>
<div>cfg.vol=vol; </div>
<div>cfg.elec=elec; %predefined; 59 electrode coordinates in MNI</div>
<div>results=sourceanalysis(cfg,data);</div>
<div> </div>
<div>Thanks,</div>
<div> </div>
<div>-Jared Van Snellenberg<br> </div>
<div><span class="gmail_quote">On 7/5/07, <b class="gmail_sendername">Robert Oostenveld</b> <<a href="mailto:r.oostenveld@fcdonders.ru.nl">r.oostenveld@fcdonders.ru.nl</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi Jared,<br><br>On 29 Jun 2007, at 3:31, Jared Van Snellenberg wrote:<br>> I'm currently working on a few DICS beamforming analyses for an EEG
<br>> dataset<br>> I have, and I have a couple of questions regarding obtaining a good<br>> volume<br>> conduction model to include in the cfg.vol input to sourceanalysis.<br>><br>> I do not have MRIs or headshape information for my subjects, but of
<br>> course<br>> I have electrode position information in spherical coordinates<br>> (stored in<br>> an elec structure imported from a BESA .elp file).<br><br>As far as I know, the BESA elp format only contains the two angles
<br>that define the electrode position in spherical coordinates (i.e. see<br><a href="http://en.wikipedia.org/wiki/Spherical_coordinates">http://en.wikipedia.org/wiki/Spherical_coordinates</a>) to project them<br>onto a spherical head model. The 3D carthesian coordinates would be
<br>more usefull and realistic (i.e. an x, y, and z value for each<br>electrode).<br><br>> It's not clear to me how to generate a volume conduction model with<br>> this<br>> information, so any guidance here would be greatly appreciated.
<br>> Ideally, I<br>> would like to use a 4-shell model.<br><br>You can use a 4-shell concentric sphere model. That is specified using<br>vol.r = [r1 r2 r3 r4] % radii of the shperes<br>vol.c = [c1 c2 c3 c4] % conductivit within each sphere
<br>vol.o = [x y z] % optional, origin of the sphere. Default is to<br>assume [0 0 0]<br><br>You can fit the radius of the outermost sphere to the electrodes. For<br>the elp files I would assume that the origin of the sphere would be
<br>[0 0 0], which means that you do not have to specify that.<br><br>The standard spherical model used in BESA is<br>vol =<br> r: [71 72 79 85]<br> c: [0.3300 1 0.0042 0.3300]<br> o: [0 0 0]<br><br>> The FIELDTRIP documentation indicates
<br>> that this model is implemented, but I can not seem to find the<br>> relevant<br>> function (and prepare_singleshell requires headshape information or<br>> an nx3<br>> sensor array--I presume in grid coordinates--that I do not have).
<br><br>The prepare_localspheres and prepare_singleshell are indeed for MEG<br>volume conductors. They can use a polhemus scanned surface of the<br>head, or a large set of points on the brain (from an MRI) or they can<br>
use a segmented anatomical MRI.<br><br>> Finally,<br>> all of the relevant prepare_XXX functions seem to indicate that<br>> they are<br>> specifically for MEG data, so I wanted to make sure that whatever<br>> approach
<br>> I use is appropriate for EEG electrodes rather than MEG sensors.<br><br>You can also use a standard realistic EEG model using the boundary<br>element method (BEM), which is based on the SPM/MNI template brain.<br>
That is not included by default in the fieldtrip release version but<br>I have just copied it as a seperate file to our ftp server. You can<br>find it on <a href="ftp://ftp.fcdonders.nl/pub/fieldtrip/standard_BEM.zip">ftp://ftp.fcdonders.nl/pub/fieldtrip/standard_BEM.zip
</a><br><br>best regards,<br>Robert<br><br>----------------------------------<br>The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also
<a href="http://listserv.surfnet.nl/archives/fieldtrip.html">http://listserv.surfnet.nl/archives/fieldtrip.html</a> and <a href="http://www.ru.nl/fcdonders/fieldtrip">http://www.ru.nl/fcdonders/fieldtrip</a>.<br></blockquote>
</div><br><br clear="all"><br>-- <br>Jared Van Snellenberg<br>Social Cognitive Affective Neuroscience Unit<br><a href="http://scan.psych.columbia.edu">http://scan.psych.columbia.edu</a><br>(212) 854-7858 p<br>(212) 854-3609 f
<br>Department of Psychology, Columbia University<br>406 Schermerhorn Hall<br>1190 Amsterdam Avenue, Mail Code 5501<br>New York, NY 10027<br>_______________________________<br>"Luck is the residue of design"<br>
-Attributed to Branch Rickey, former US Baseball Administrator, and also to John Milton. Go figure.
<p>----------------------------------</p>
<p>The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis.</p>
<p> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>