<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Susmita,<div class=""><br class=""></div><div class="">I think first all </div><div class=""><a href="http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined" class="">http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined</a> </div><div class="">is a nice place to go to understand the different coordinate systems.</div><div class=""><br class=""></div><div class="">I’m not to well aware about the Yokogawa coordinate system, but my first expectation would be that this coordinate systems is shifted lower than the CTF. After aligning with the different coordinate systems you should look at mri_aligned.coordsys</div><div class=""><br class=""></div><div class="">Best regards, </div><div class=""><br class=""></div><div class=""><div class="">
Simon Homölle<br class="">PhD Candidate<br class="">Donders Institute for Brain, Cognition and Behaviour<br class="">Centre for Cognitive Neuroimaging<br class="">Radboud University Nijmegen<br class="">Phone: +31-(0)24-36-65059
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<br class=""><div><blockquote type="cite" class=""><div class="">On 03 Oct 2016, at 14:59, Susmita Sen <<a href="mailto:susmitasen.ece@gmail.com" class="">susmitasen.ece@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div dir="ltr" class="">Dear Simon,<div class=""><br class=""></div><div class="">Thank you very much for your response. I am sorry to bother you once again with my doubt. The headmodel that I have constructed, has a flat surface at the bottom. I would like to ask you to explain why that is happening. If I use 'ctf' instead of 'yokogawa', the heamodel does not look like this. I am attaching a file comparing these two headmodels. I have circled some part of the figure which actually raises the question of whether I am doing it correctly or not. Is there anything wrong in choosing the <span style="font-size:12.8px" class="">fiducial </span>points? Thank you in anticipation.</div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="m_-3722881428665042206gmail-m_-3083814458218946758gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class="">Thanks and Regards,<div class="">Susmita Sen</div><div class="">Research Scholar</div><div class="">Audio and Bio Signal Processing Lab.</div><div class="">E & ECE Dept.</div><div class="">IIT Kharagpur</div></div></div></div></div></div>
<br class=""><div class="gmail_quote">On Mon, Oct 3, 2016 at 1:49 PM, Simon Homolle <span dir="ltr" class=""><<a href="mailto:s.homolle@donders.ru.nl" target="_blank" class="">s.homolle@donders.ru.nl</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word" class="">Dear Susmita,<div class=""><br class=""></div><div class="">I used your code and could reproduce the same results. The step that goes wrong here is the segmentation step.</div><div class=""><br class=""></div><div class=""><div style="margin:0px;font-size:10px;line-height:normal;font-family:courier" class=""><div style="margin:0px;line-height:normal" class="">cfg = [];</div><div style="margin:0px;line-height:normal" class="">cfg.output = {<span style="color:rgb(178,69,243)" class="">'brain'</span>,<span style="color:rgb(178,69,243)" class="">'skull'</span>,<span style="color:rgb(178,69,243)" class="">'scalp'</span>};</div><div style="margin:0px;line-height:normal" class="">segmentedmri = ft_volumesegment(cfg, mri_aligned);</div><div style="margin: 0px; line-height: normal; min-height: 12px;" class=""> <br class="m_-3722881428665042206gmail-m_-3083814458218946758m_-5344865772169775344webkit-block-placeholder"></div><div style="margin:0px;line-height:normal" class="">seg_i = ft_datatype_segmentation(segme<wbr class="">ntedmri,<span style="color:rgb(178,69,243)" class="">'segmentationstyle'</span>,<span style="color:rgb(178,69,243)" class="">'i<wbr class="">ndexed'</span>);</div><div style="margin: 0px; line-height: normal; min-height: 12px;" class=""> <br class="m_-3722881428665042206gmail-m_-3083814458218946758m_-5344865772169775344webkit-block-placeholder"></div><div style="margin:0px;line-height:normal" class="">cfg = [];</div><div style="margin:0px;line-height:normal" class="">cfg.funparameter = <span style="color:rgb(178,69,243)" class="">'seg'</span>;</div><div style="margin:0px;line-height:normal" class="">cfg.funcolormap = lines(6); <span style="color:rgb(37,153,45)" class="">% distinct color per tissue</span></div><div style="margin:0px;line-height:normal" class="">cfg.location = <span style="color:rgb(178,69,243)" class="">'center'</span>;</div><div style="margin:0px;line-height:normal;color:rgb(37,153,45)" class=""><span style="" class="">cfg.atlas = seg_i; </span>% the segmentation can also be used as atlas </div><div style="margin:0px;line-height:normal" class="">ft_sourceplot(cfg, seg_i);</div><div class=""><br class=""></div></div></div><div class=""><br class=""></div><div class="">I segmented additionally to the scalp the brain and the skull tissues as well so that you can clearly see whats going on. </div><div class=""><br class=""></div><div class="">You should tweak the cfg for the ft_volumesegment to improve your pipeline.</div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""><br class=""><div class="">
Simon Homölle<br class="">PhD Candidate<br class="">Donders Institute for Brain, Cognition and Behaviour<br class="">Centre for Cognitive Neuroimaging<br class="">Radboud University Nijmegen<br class="">Phone: +31-(0)24-36-65059
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<br class=""><div class=""><blockquote type="cite" class=""><div class=""><div class="m_-3722881428665042206gmail-m_-3083814458218946758h5"><div class="">On 30 Sep 2016, at 19:16, Susmita Sen <<a href="mailto:susmitasen.ece@gmail.com" target="_blank" class="">susmitasen.ece@gmail.com</a>> wrote:</div><br class="m_-3722881428665042206gmail-m_-3083814458218946758m_-5344865772169775344Apple-interchange-newline"></div></div><div class=""><div class=""><div class="m_-3722881428665042206gmail-m_-3083814458218946758h5"><div dir="ltr" class=""><div class=""><div style="font-size:12.8px" class="">I am Susmita Sen, MS research scholar in the dept of Electronics and Electrical Communication Engineering, IIT Kharagpur. </div><div style="font-size:12.8px" class=""> I am currently working on MEG data recorded by yokogawa system. I want to perform source reconstruction on the data. However, I do not have the MRI data along with that. so, I have planned to use the standard MRI provided by fieldtrip (downloaded from <a href="https://github.com/fieldtrip/fieldtrip/blob/master/template/headmodel/standard_mri.mat" target="_blank" class="">https://github.com/fieldt<wbr class="">rip/fieldtrip/blob/master/temp<wbr class="">late/headmodel/standard_mri.<wbr class="">mat</a>).<br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">For preparing the head model I have followed the steps provided in the fieldtrip tutorial (<a href="http://www.fieldtriptoolbox.org/tutorial/headmodel_meg" target="_blank" class="">http://www.fieldtriptoolbox.o<wbr class="">rg/tutorial/headmodel_meg</a>). </div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><div class="">%% align the coordinate system</div><div class="">load('standard_mri.mat'); % load mri data</div><div class="">disp(mri)</div><div class=""><br class=""></div><div class="">cfg = [];</div><div class="">cfg.method = 'interactive';</div><div class="">cfg.coordsys = 'yokogawa';</div><div class="">cfg.snapshot = 'yes';</div><div class="">[mri_aligned] = ft_volumerealign(cfg,mri);</div><div class=""><br class=""></div><div class="">%% SEGMENTATION</div><div class="">cfg = [];</div><div class="">cfg.output = 'brain';</div><div class="">segmentedmri = ft_volumesegment(cfg, mri_aligned);</div><div class=""><br class=""></div><div class="">%% create headmodel</div><div class="">cfg = [];</div><div class="">cfg.method='singleshell';</div><div class="">vol = ft_prepare_headmodel(cfg, segmentedmri);</div><div class=""><br class=""></div><div class="">%% visualize </div><div class="">load grad % load gradiometer info</div><div class="">vol = ft_convert_units(vol,'cm'); % the gradiometer info is given in cm</div><div class=""><br class=""></div><div class="">figure;</div><div class="">ft_plot_sens(grad, 'style', '*b');</div><div class="">hold on</div><div class="">ft_plot_vol(vol);</div></div><div style="font-size:12.8px" class=""> </div><div style="font-size:12.8px" class="">while aligning the coordinate system I have chosen fiducial points (naison, LPA and RPA) using the instruction given by <a href="http://neuroimage.usc.edu/brainstorm/CoordinateSystems" target="_blank" class="">http://neuroimage.usc.edu/b<wbr class="">rainstorm/CoordinateSystems</a>.</div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">I am attaching the figures that display the shape of the 'vol' along with the position of the sensors (from different viewing angle). However, I doubt the headmodel is corrected prepared (It dosen't look alike the figure given in the tutorial). It seems I have made some mistakes, but I am not able to detect it. I would be very thankful if you can help me in this regard. </div><div style="font-size:12.8px" class=""><br class=""></div></div><div class=""><br class=""></div><br clear="all" class=""><div class=""><div class="m_-3722881428665042206gmail-m_-3083814458218946758m_-5344865772169775344gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class="">Thanks and Regards,<div class="">Susmita Sen</div><div class="">Research Scholar</div><div class="">Audio and Bio Signal Processing Lab.</div><div class="">E & ECE Dept.</div><div class="">IIT Kharagpur</div></div></div></div></div></div>
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