<div dir="ltr">Dear Simon,<div><br></div><div>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">fiducial </span>points? Thank you in anticipation.</div><div class="gmail_extra"><br clear="all"><div><div class="m_-3722881428665042206gmail-m_-3083814458218946758gmail_signature"><div dir="ltr"><div><div dir="ltr">Thanks and Regards,<div>Susmita Sen</div><div>Research Scholar</div><div>Audio and Bio Signal Processing Lab.</div><div>E & ECE Dept.</div><div>IIT Kharagpur</div></div></div></div></div></div>
<br><div class="gmail_quote">On Mon, Oct 3, 2016 at 1:49 PM, Simon Homolle <span dir="ltr"><<a href="mailto:s.homolle@donders.ru.nl" target="_blank">s.homolle@donders.ru.nl</a>></span> wrote:<br><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">Dear Susmita,<div><br></div><div>I used your code and could reproduce the same results. The step that goes wrong here is the segmentation step.</div><div><br></div><div><div style="margin:0px;font-size:10px;line-height:normal;font-family:courier"><div style="margin:0px;line-height:normal">cfg = [];</div><div style="margin:0px;line-height:normal">cfg.output = {<span style="color:rgb(178,69,243)">'brain'</span>,<span style="color:rgb(178,69,243)">'skull'</span>,<span style="color:rgb(178,69,243)">'scalp'</span>};</div><div style="margin:0px;line-height:normal">segmentedmri = ft_volumesegment(cfg, mri_aligned);</div><p style="margin:0px;line-height:normal;min-height:12px"> <br class="m_-3722881428665042206gmail-m_-3083814458218946758m_-5344865772169775344webkit-block-placeholder"></p><div style="margin:0px;line-height:normal">seg_i = ft_datatype_segmentation(segme<wbr>ntedmri,<span style="color:rgb(178,69,243)">'segmentationstyle'</span>,<span style="color:rgb(178,69,243)">'i<wbr>ndexed'</span>);</div><p style="margin:0px;line-height:normal;min-height:12px"> <br class="m_-3722881428665042206gmail-m_-3083814458218946758m_-5344865772169775344webkit-block-placeholder"></p><div style="margin:0px;line-height:normal">cfg = [];</div><div style="margin:0px;line-height:normal">cfg.funparameter = <span style="color:rgb(178,69,243)">'seg'</span>;</div><div style="margin:0px;line-height:normal">cfg.funcolormap = lines(6); <span style="color:rgb(37,153,45)">% distinct color per tissue</span></div><div style="margin:0px;line-height:normal">cfg.location = <span style="color:rgb(178,69,243)">'center'</span>;</div><div style="margin:0px;line-height:normal;color:rgb(37,153,45)"><span style="color:rgb(0,0,0)">cfg.atlas = seg_i; </span>% the segmentation can also be used as atlas </div><div style="margin:0px;line-height:normal">ft_sourceplot(cfg, seg_i);</div><div><br></div></div></div><div><br></div><div>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><br></div><div>You should tweak the cfg for the ft_volumesegment to improve your pipeline.</div><div><br></div><div>Best regards,</div><div><br><div>
Simon Homölle<br>PhD Candidate<br>Donders Institute for Brain, Cognition and Behaviour<br>Centre for Cognitive Neuroimaging<br>Radboud University Nijmegen<br>Phone: +31-(0)24-36-65059
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<br><div><blockquote type="cite"><div><div class="m_-3722881428665042206gmail-m_-3083814458218946758h5"><div>On 30 Sep 2016, at 19:16, Susmita Sen <<a href="mailto:susmitasen.ece@gmail.com" target="_blank">susmitasen.ece@gmail.com</a>> wrote:</div><br class="m_-3722881428665042206gmail-m_-3083814458218946758m_-5344865772169775344Apple-interchange-newline"></div></div><div><div><div class="m_-3722881428665042206gmail-m_-3083814458218946758h5"><div dir="ltr"><div><div style="font-size:12.8px">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"> 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">https://github.com/fieldt<wbr>rip/fieldtrip/blob/master/temp<wbr>late/headmodel/standard_mri.<wbr>mat</a>).<br></div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">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">http://www.fieldtriptoolbox.o<wbr>rg/tutorial/headmodel_meg</a>). </div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px"><div>%% align the coordinate system</div><div>load('standard_mri.mat'); % load mri data</div><div>disp(mri)</div><div><br></div><div>cfg = [];</div><div>cfg.method = 'interactive';</div><div>cfg.coordsys = 'yokogawa';</div><div>cfg.snapshot = 'yes';</div><div>[mri_aligned] = ft_volumerealign(cfg,mri);</div><div><br></div><div>%% SEGMENTATION</div><div>cfg = [];</div><div>cfg.output = 'brain';</div><div>segmentedmri = ft_volumesegment(cfg, mri_aligned);</div><div><br></div><div>%% create headmodel</div><div>cfg = [];</div><div>cfg.method='singleshell';</div><div>vol = ft_prepare_headmodel(cfg, segmentedmri);</div><div><br></div><div>%% visualize </div><div>load grad % load gradiometer info</div><div>vol = ft_convert_units(vol,'cm'); % the gradiometer info is given in cm</div><div><br></div><div>figure;</div><div>ft_plot_sens(grad, 'style', '*b');</div><div>hold on</div><div>ft_plot_vol(vol);</div></div><div style="font-size:12.8px"> </div><div style="font-size:12.8px">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">http://neuroimage.usc.edu/b<wbr>rainstorm/CoordinateSystems</a>.</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">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"><br></div></div><div><br></div><br clear="all"><div><div class="m_-3722881428665042206gmail-m_-3083814458218946758m_-5344865772169775344gmail_signature"><div dir="ltr"><div><div dir="ltr">Thanks and Regards,<div>Susmita Sen</div><div>Research Scholar</div><div>Audio and Bio Signal Processing Lab.</div><div>E & ECE Dept.</div><div>IIT Kharagpur</div></div></div></div></div></div>
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