<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Jeff,<div><br></div><div>Thanks for reporting this. We'll look into it as soon as possible.</div><div><br></div><div>Best wishes,</div><div><br></div><div>Jan-Mathijs</div><div><br></div><div><br><div><div>On May 30, 2011, at 11:28 PM, Jeff Stout wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><table cellspacing="0" cellpadding="0" border="0"><tbody><tr><td valign="top" style="font: inherit;"><div id="yiv529153451"><table cellspacing="0" cellpadding="0" border="0" id="yiv529153451bodyDrftID" class="yiv529153451"><tbody><tr><td id="yiv529153451drftMsgContent" style="font: inherit; "><font class="Apple-style-span" size="2">Hi All,</font><div style="font-family: arial; font-size: 10pt; "><br></div><div style="font-family: arial; font-size: 10pt; ">I am having trouble using the ft_megrealign command with a 4D Magnes 3600 system. I am trying to use this command to interpolate bad channels that have been removed in preprocessing. When I view the output of megrealign using ft_plot_sens, sensor 'A229' is badly misplaced (approximately 10 cm above the top of the sensor array), but all the other sensors appear appropriate. In the dataset A229 has not been labelled as a bad channel, nor any of its neighboring channels. The location of A229 is significant in that it is the most inferior/anterior channel on the left side. I am using the original grad file as a template input using ft_read_sens('c,rfDC') and scaling the MEG channels to cm. I am not sure how helpful the code is - below is my input and some of the output. I can provide an image if this would be helpful.</div><div style="font-family: arial; font-size: 10pt; "><br></div><div style="font-family: arial; font-size: 10pt; "><span class="yiv529153451Apple-style-span" style="font-family:arial, helvetica, clean, sans-serif;line-height:15px;"><table cellspacing="0" cellpadding="0" border="0" style="border-collapse:collapse;font-size:inherit;line-height:1.2em;outline-style:none;outline-color:initial;display:table;"><tbody style="line-height:1.2em;outline-style:none;outline-color:initial;"><tr style="line-height:1.2em;outline-style:none;outline-color:initial;display:table-row;vertical-align:inherit;"><td valign="top" style="line-height:1.2em;outline-style:none;outline-color:initial;display:table-cell;font:inherit;"><br style="line-height:1.2em;outline-style:none;outline-color:initial;">temp = ft_read_sens(subjectdata.FA_dataset);<br style="line-height:1.2em;outline-style:none; outline-color:initial;">temp.pnt = temp.pnt*100;<br style="line-height:1.2em;outline-style:none;outline-color:initial;">temp.unit = 'cm';<br style="line-height:1.2em;outline-style:none;outline-color:initial;"><br style="line-height:1.2em;outline-style:none;outline-color:initial;">cfg = [];<br style="line-height:1.2em;outline-style:none;outline-color:initial;">cfg.inwardshift = 1;<br style="line-height:1.2em;outline-style:none;outline-color:initial;">cfg.vol=vol;<br style="line-height:1.2em;outline-style:none;outline-color:initial;">cfg.template{1}= temp;<br style="line-height:1.2em;outline-style:none;outline-color:initial;">cfg.channel={'MEG'};<br style="line-height:1.2em;outline-style:none;outline-color:initial;">con.grad.pnt = con.grad.pnt*100;<br style="line-height:1.2em;outline-style:none;outline-color:initial;">con.grad.unit = 'cm';<br style="line-height:1.2em;outline-style:none;outline-color:initial;">con = ft_megrealign(cfg, con)<br style="line-height:1.2em;outline-style:none;outline-color:initial;"><br style="line-height:1.2em;outline-style:none;outline-color:initial;">computing <span class="yiv529153451yshortcuts" id="yiv529153451lw_1306789497_0" style="line-height:1.2em;outline-style:none;outline-color:initial;border-bottom-style:dotted;border-bottom-width:2px;border-bottom-color:rgb(54, 99, 136);cursor:pointer;background-color:transparent; ">surface normals</span><br style="line-height:1.2em;outline-style:none;outline-color:initial;">mean distance towards template gradiometers is 0.00 cm<br style="line-height:1.2em;outline-style:none;outline-color:initial;">creating dipole grid based on inward-shifted brain surface from volume conductor model<br style="line-height:1.2em;outline-style:none;outline-color:initial;">Warning: the normals of the surface triangulation are inward oriented <br style="line-height:1.2em;outline-style:none;outline-color:initial;">> In fieldtrip-20110507/private/headsurface at 211<br style="line-height:1.2em;outline-style:none;outline-color:initial;"> In ft_prepare_sourcemodel at 492<br style="line-height:1.2em;outline-style:none;outline-color:initial;"> In ft_megrealign at 245<br style="line-height:1.2em;outline-style:none;outline-color:initial;">642 dipoles inside, 0 dipoles outside brain<br style="line-height:1.2em;outline-style:none;outline-color:initial;">computing forward model for 642 dipoles<br style="line-height:1.2em;outline-style:none;outline-color:initial;">pruning 122 from 246, i.e. removing the 122 smallest spatial components<br style="line-height:1.2em;outline-style:none;outline-color:initial;">computing interpolation matrix #1<br style="line-height:1.2em;outline-style:none;outline-color:initial;">computing interpolation matrix #2<br style="line-height:1.2em;outline-style:none;outline-color:initial;">computing interpolation matrix #3<br style="line-height:1.2em;outline-style:none;outline-color:initial;">pruning 124 from 248, i.e. removing the 124 smallest spatial components<br style="line-height:1.2em;outline-style:none;outline-color:initial;">realigning trial 1<br style="line-height:1.2em;outline-style:none;outline-color:initial;">original -> template RV 14.42 %<br style="line-height:1.2em;outline-style:none;outline-color:initial;">original -> original RV 14.42 %<br style="line-height:1.2em;outline-style:none;outline-color:initial;">original -> template -> original RV 14.44 % ....................<br><br><br><span class="Apple-style-span" style="font-family: arial; border-collapse: separate; line-height: normal; font-size: medium; "><div><font class="Apple-style-span" size="2">Does anyone know why this would be occurring and how to fix it?</font></div><div><font class="Apple-style-span" size="2"><br></font></div><div><font class="Apple-style-span" size="2">Thanks,<br>Jeff Stout</font></div></span><br></td></tr></tbody></table></span></div></td></tr></tbody></table></div></td></tr></tbody></table>_______________________________________________<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</blockquote></div><br><div apple-content-edited="true"> <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: 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-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>Dr. J.M. (Jan-Mathijs) Schoffelen </div><div>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands</div><div><a href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a></div><div>Telephone: 0031-24-3614793</div></div></span></div></span> </div><br></div></body></html>