<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hey Guys,
<div class=""><br class="">
</div>
<div class="">I am trying to create a head model using a template anatomical MRI and the fiducial points included in my CTF MEG data. However, when I include the fiducial points as returned by ft_read_heashape, it causes the head model and sensors to be completely
misaligned (see attached photo). I have tried with and without converting them both into mm units using ft_convert_units but this did not help. The process works if I use the interactive method in ft_volumerealign so I’m sure the error is coming at this point.
The reason I do not want to use the interactive method is because if I do that I will end up with one head model for all subjects (as I would just be clicking on the same fiducial points for each subject). I want to use the fiducial points measured by the
MEG system per subject, to improve the fit of the head model for each subject. I’ve included my code below. </div>
<div class=""><br class="">
</div>
<div class="">Would you be able to help me figure out how to use subject specific, MEG-measured fiducial points in the volume realignment step of the forward-model process? Thank you.</div>
<div class=""><br class="">
</div>
<div class="">
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(170, 4, 249);" class="">
<span style="color: #000000" class="">mri = ft_read_mri(</span>‘~\template\anatomy\single_subj_T1.nii'<span style="color: #000000" class="">);</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; min-height: 13px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(2, 128, 9);" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; min-height: 13px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(2, 128, 9);" class="">
%get fiducial points</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(170, 4, 249);" class="">
<span style="color: #000000" class="">raw_data_dir = fullfile(</span>‘~\data\Raw'<span style="color: #000000" class="">,subject,</span>'meg'<span style="color: #000000" class="">,</span>'raw'<span style="color: #000000" class="">);</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><font face="Courier" class=""><span style="font-size: 11px;" class="">dataSets = str2fullfile(raw_data_dir,</span></font><font color="#aa04f9" face="Courier" class=""><span style="caret-color: rgb(170, 4, 249); font-size: 11px;" class="">’</span><span style="font-size: 11px;" class="">*wildcard*'</span></font><font face="Courier" class=""><span style="font-size: 11px;" class="">);</span></font></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
ds = dataSets(1);</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
head = ft_read_headshape(ds);</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">head = ft_convert_units(head,<span style="color: rgb(243, 35, 255);" class="">'mm'</span>);</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 13px;" class="">
<br class="">
</div>
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; min-height: 13px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; min-height: 13px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(2, 128, 9);" class="">
%align to ctf</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
cfg = [];</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
cfg.method = <span style="color: #aa04f9" class="">'fiducial'</span>;</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
cfg.coordsys = <span style="color: #aa04f9" class="">'ctf'</span>;</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
cfg.fiducial.nas = head.fid.pos(1,:);</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
cfg.fiducial.lpa = head.fid.pos(2,:);</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
cfg.fiducial.rpa = head.fid.pos(3,:);</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
mri_realigned = ft_volumerealign(cfg,mri);</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; min-height: 13px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; min-height: 13px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; min-height: 13px;" class="">
%And then the rest of the code to create the head model, which I believe is correct.</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; min-height: 13px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(2, 128, 9);" class="">
%segment brain from skull</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
cfg = [];</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
cfg.output = <span style="color: #aa04f9" class="">'brain'</span>;</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
segmentedmri = ft_volumesegment(cfg, mri_realigned);</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(2, 128, 9);" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(2, 128, 9);" class="">
% Build volume conduction model from geometry of brain</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
cfg = [];</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(170, 4, 249);" class="">
<span style="color: #000000" class="">cfg.method=</span>'singleshell'<span style="color: #000000" class="">;</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
vol = ft_prepare_headmodel(cfg, segmentedmri);</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; min-height: 13px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(2, 128, 9);" class="">
% Visualise</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
vol = ft_convert_units(vol, <span style="color: #aa04f9" class="">'cm'</span>);</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
sens = ft_read_sens(ds{1}, <span style="color: #aa04f9" class="">'senstype'</span>,
<span style="color: #aa04f9" class="">'meg'</span>);</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
figure</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(170, 4, 249);" class="">
<span style="color: #000000" class="">ft_plot_sens(sens, </span>'coilshape'<span style="color: #000000" class="">,</span>'point'<span style="color: #000000" class="">,</span>'style'<span style="color: #000000" class="">,
</span>'r+'<span style="color: #000000" class="">);</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier; min-height: 13px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
hold <span style="color: #aa04f9" class="">on</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Courier;" class="">
ft_plot_headmodel(vol);</div>
</div>
<div class=""><img apple-inline="yes" id="9688FD28-8FB7-4BD3-AF96-2DEAA12819D6" width="305" height="229" src="cid:0A5F1B61-897A-45A3-8BFF-B7E25928C878@cust.communityfibre.co.uk" class=""></div>
</body>
</html>