<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ying,<div><br></div><div>Yes, it's possible to constrain the dipole orientation. If you have a cortical sheet based source model that contains a triangulation that describes the topology, it's in principle possible to compute the orientation perpendicular to the sheet (this can e.g. be done by the 'normals' function which I believe should be in ~/fieldtrip/private). Subsequently, for each vertex in the cortical sheet you can multiply the leadfield matrix with this vector to get a single column leadfield vector per vertex that describes the sensor topography of a dipolar source with orientation perpendicular to the cortex.</div><div><br></div><div>Best,</div><div>Jan-Mathijs</div><div><br><div><div>On May 22, 2014, at 11:04 AM, Eelke Spaak wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Ying,<br><br>In addition to this, of course first you would need a model of the<br>cortical surface for your subjects. See<br><a href="http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate">http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate</a> for how to<br>obtain such a model (using FreeSurfer) and getting it into FieldTrip.<br><br>Best,<br>Eelke<br><br>On 22 May 2014 10:56, "Jörn M. Horschig" <<a href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>> wrote:<br><blockquote type="cite">Hi Ying,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">when computing the leadfields you can set the option cfg.reducerank, which<br></blockquote><blockquote type="cite">'nulls' the dimension(s) which explain(s) the least variance (this is not<br></blockquote><blockquote type="cite">quite true, but figuratively speaking). I think this is what comes closest<br></blockquote><blockquote type="cite">to what you are looking for. There is no way to explicitly set desired<br></blockquote><blockquote type="cite">orientations to zero apart from modifying the leadfield structure yourself.<br></blockquote><blockquote type="cite">But that should be easily achievable, right?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best,<br></blockquote><blockquote type="cite">Jörn<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On 5/22/2014 10:26 AM, Ying Li wrote:<br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Dear all,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I tried to use fieldtrip to generate a source space and calculate lead<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">field matrix. I found that the dipoles in the source space has x, y, z<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">orientations. Is it possible to generate a source model where the dipole is<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">perpendicular to the cortex surface?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Actually this can be very helpful, since it will reduce the unknown<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">variables and make the inverse problem easier to solve. Also, there are some<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">inverse algorithms which require the dipole to be perpendicular to the<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">cortex surface.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks a lot!!!<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Best,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Ying<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">fieldtrip mailing list<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">Jörn M. Horschig<br></blockquote><blockquote type="cite">PhD Student<br></blockquote><blockquote type="cite">Donders Institute for Brain, Cognition and Behaviour<br></blockquote><blockquote type="cite">Centre for Cognitive Neuroimaging<br></blockquote><blockquote type="cite">Radboud University Nijmegen<br></blockquote><blockquote type="cite">Neuronal Oscillations Group<br></blockquote><blockquote type="cite">FieldTrip Development Team<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">P.O. Box 9101<br></blockquote><blockquote type="cite">NL-6500 HB Nijmegen<br></blockquote><blockquote type="cite">The Netherlands<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Contact:<br></blockquote><blockquote type="cite">E-Mail: <a href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a><br></blockquote><blockquote type="cite">Tel: +31-(0)24-36-68493<br></blockquote><blockquote type="cite">Web: <a href="http://www.ru.nl/donders">http://www.ru.nl/donders</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Visiting address:<br></blockquote><blockquote type="cite">Trigon, room 2.30<br></blockquote><blockquote type="cite">Kapittelweg 29<br></blockquote><blockquote type="cite">NL-6525 EN Nijmegen<br></blockquote><blockquote type="cite">The Netherlands<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">fieldtrip mailing list<br></blockquote><blockquote type="cite"><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br></blockquote><blockquote type="cite"><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br></blockquote><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</div></blockquote></div><br><div>
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font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Jan-Mathijs Schoffelen, MD PhD </div><div><br></div><div>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands</div><div><br></div><div>Max Planck Institute for Psycholinguistics,</div><div>Nijmegen, The Netherlands</div><div><br></div><div><a href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a></div><div>Telephone: +31-24-3614793</div><div><br></div><div><a href="http://www.hettaligebrein.nl">http://www.hettaligebrein.nl</a></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></span>
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