<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10pt"><div style="" class=""><span style="" class="">Dear </span>Jörn,</div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue-Light,Helvetica Neue Light,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;" class="">thank you for your reply, actually I didn't send many emails because I didn't receive any reply directly, the problem was that each time I sent the email I received a failure email mentioning that my email was not delivered so I had to resent it again. My apologies for this I don't know what was the problem. <br></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue-Light,Helvetica Neue Light,Helvetica Neue,Helvetica,Arial,Lucida
Grande,sans-serif; background-color: transparent; font-style: normal;" class="">I will follow your advise hoping to get some results.</div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue-Light,Helvetica Neue Light,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;" class="">Regards</div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue-Light,Helvetica Neue Light,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;" class="">Rasha<br></div><div style="" class=""><br style="" class=""></div> <div class="" style="font-family: HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 10pt;"> <div class="" style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 12pt;"> <div
style="" class="" dir="ltr"> <hr style="" class="" size="1"> <font style="" class="" face="Arial" size="2"> <b style="" class=""><span class="" style="font-weight:bold;">From:</span></b> Jörn M. Horschig <jm.horschig@donders.ru.nl><br style="" class=""> <b style="" class=""><span class="" style="font-weight: bold;">To:</span></b> FieldTrip discussion list <fieldtrip@science.ru.nl> <br style="" class=""> <b style="" class=""><span class="" style="font-weight: bold;">Sent:</span></b> Tuesday, July 8, 2014 4:00 PM<br style="" class=""> <b style="" class=""><span class="" style="font-weight: bold;">Subject:</span></b> Re: [FieldTrip] Coregistration using fixed fiducials coordinates<br style="" class=""> </font> </div> <div style="" class=""><br style="" class="">Hi Rasha,<br style="" class="" clear="none"><br style="" class="" clear="none">you can call ft_determine_coordsys, or set the field manually if you <br style="" class=""
clear="none">what coordinate system the MRI is in.<br style="" class="" clear="none"><br style="" class="" clear="none">You could have also used the search function of the fieldtrip wiki (on <br style="" class="" clear="none">the upper right on the page), e.g. by searching for coordinate system:<br style="" class="" clear="none"><a style="" class="" shape="rect" href="http://fieldtrip.fcdonders.nl/?do=search&id=coordinate+system" target="_blank">http://fieldtrip.fcdonders.nl/?do=search&id=coordinate+system</a><br style="" class="" clear="none">This leads to a page that lists all pages on which the term coordinate <br style="" class="" clear="none">system occur. You can see that the first match links to a FAQ, which <br style="" class="" clear="none">also hints to ft_determine_coordsys. FAQs can also be found when <br style="" class="" clear="none">navigating to "User documentation" and then "Frequently asked <br style="" class=""
clear="none">questions". We spent quite some time to list a number of questions and <br style="" class="" clear="none">detailled answers there. The answers are mostly more extensive than the <br style="" class="" clear="none">question alone, so any question that might be remotely related to your <br style="" class="" clear="none">actual question might be of interest there.<br style="" class="" clear="none"><br style="" class="" clear="none">However, please don't be afraid to ask any further questions, just <br style="" class="" clear="none">notice that we're all doing this here besides our research, so sometimes <br style="" class="" clear="none">it might take a bit longer for us to respond than within a few hours. <br style="" class="" clear="none">Any search that you do in advance on the FT wiki is time that we do not <br style="" class="" clear="none">have to spend ;) So, please don't send the same message five times <br style="" class=""
clear="none">within not even a week, once a week should be enough ;)<br style="" class="" clear="none"><br style="" class="" clear="none">Best,<br style="" class="" clear="none">Jörn<br style="" class="" clear="none"><div style="" class="" id="yqtfd69601"><br style="" class="" clear="none">On 7/8/2014 6:44 AM, Rasha Haider wrote:<br style="" class="" clear="none">> Dear fieldtrip experts,<br style="" class="" clear="none">> Im trying to do source localization for simulated EEG data, for this I <br style="" class="" clear="none">> followed the tutorial in page:<br style="" class="" clear="none">> <a style="" class="" shape="rect" href="http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate" target="_blank">http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate</a><br style="" class="" clear="none">><br style="" class="" clear="none">> I was trying to use the mri image provided by fieldtrip <br style="" class=""
clear="none">> (Subject01.mri) and EEG template (standard_1020.elc) in my work.<br style="" class="" clear="none">> The mri image need to be re-aliened to the Talairach space for <br style="" class="" clear="none">> coregistration with EEG space. In the tutorial you use <br style="" class="" clear="none">> (ft_volumerealien) to do that using interactive method.<br style="" class="" clear="none">> I have two questions:<br style="" class="" clear="none">><br style="" class="" clear="none">> First, how can I do the coregistration using fixed coordinates of the <br style="" class="" clear="none">> 3 fiducials (nasion, left pr, right pr), in other words how can I get <br style="" class="" clear="none">> the coordinates of the fiducials in both Talairach and EEG spaces to <br style="" class="" clear="none">> do the coregistration using the script only not manually.<br style="" class="" clear="none">><br style="" class=""
clear="none">> Second, I tried to use the mri image provided by the spm toolbox <br style="" class="" clear="none">> because its already aliened to Talairach space, but when I try to do <br style="" class="" clear="none">> segmentation I get error that coordinates field does not exist:<br style="" class="" clear="none">><br style="" class="" clear="none">> ??? Reference to non-existent field 'coordsys'.<br style="" class="" clear="none">><br style="" class="" clear="none">> Error in ==> ft_volumesegment at 284<br style="" class="" clear="none">> original.coordsys = mri.coordsys;<br style="" class="" clear="none">><br style="" class="" clear="none">> Error in ==> segmentation_spm_mri at 24<br style="" class="" clear="none">> seg = ft_volumesegment(cfg, mrirs);<br style="" class="" clear="none">><br style="" class="" clear="none">> I read the image using
(ft_read_mri) function, I don't find the field <br style="" class="" clear="none">> specified for the coordinates:<br style="" class="" clear="none">><br style="" class="" clear="none">> disp(mri)<br style="" class="" clear="none">> dim: [177 240 256]<br style="" class="" clear="none">> anatomy: [177x240x256 double]<br style="" class="" clear="none">> hdr: [1x1 struct]<br style="" class="" clear="none">> transform: [4x4 double]<br style="" class="" clear="none">> unit: 'mm'<br style="" class="" clear="none">><br style="" class="" clear="none">> How can I solve this problem so I can use the mri image in SPM for <br style="" class="" clear="none">> further analysing in fieldtrip?<br style="" class="" clear="none">><br style="" class="" clear="none">> Sorry for the long email I
would be thankful for any help.<br style="" class="" clear="none">> Regards<br style="" class="" clear="none">> Rasha</div><br style="" class="" clear="none">><br style="" class="" clear="none">><br style="" class="" clear="none">><br style="" class="" clear="none">><br style="" class="" clear="none">> _______________________________________________<br style="" class="" clear="none">> fieldtrip mailing list<br style="" class="" clear="none">> <a style="" class="" shape="rect" ymailto="mailto:fieldtrip@donders.ru.nl" href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br style="" class="" clear="none">> <a style="" class="" shape="rect" href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="" class="" clear="none"><br style="" class="" clear="none"><br style="" class="" clear="none">-- <br style="" class=""
clear="none">Jörn M. Horschig<br style="" class="" clear="none">PhD Student<br style="" class="" clear="none">Donders Institute for Brain, Cognition and Behaviour<br style="" class="" clear="none">Centre for Cognitive Neuroimaging<br style="" class="" clear="none">Radboud University Nijmegen<br style="" class="" clear="none">Neuronal Oscillations Group<br style="" class="" clear="none">FieldTrip Development Team<br style="" class="" clear="none"><br style="" class="" clear="none">P.O. Box 9101<br style="" class="" clear="none">NL-6500 HB Nijmegen<br style="" class="" clear="none">The Netherlands<br style="" class="" clear="none"><br style="" class="" clear="none">Contact:<br style="" class="" clear="none">E-Mail: <a style="" class="" shape="rect" ymailto="mailto:jm.horschig@donders.ru.nl" href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a><br style="" class="" clear="none">Tel: +31-(0)24-36-68493<br style="" class=""
clear="none">Web: <a style="" class="" shape="rect" href="http://www.ru.nl/donders" target="_blank">http://www.ru.nl/donders</a><br style="" class="" clear="none"><br style="" class="" clear="none">Visiting address:<br style="" class="" clear="none">Trigon, room 2.30<br style="" class="" clear="none">Kapittelweg 29<br style="" class="" clear="none">NL-6525 EN Nijmegen<br style="" class="" clear="none">The Netherlands<br style="" class="" clear="none"><br style="" class="" clear="none">_______________________________________________<br style="" class="" clear="none">fieldtrip mailing list<br style="" class="" clear="none"><a style="" class="" shape="rect" ymailto="mailto:fieldtrip@donders.ru.nl" href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br style="" class="" clear="none"><a style="" class="" shape="rect" href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="" class=""><br style="" class=""></div> </div> </div> </div></body></html>