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Dear Susmita,
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<div class="">It looks as if there is a discrepancy between the definition of the coordinate system according to fieldtrip (see ft_headcoordinates in fieldtrip/utilities, where it seems that an ALS axis system is imposed), when specifying cfg.coordsys = ‘yokogawa’,
and the coordinate system of the sensors in your data file (which is probably RAS). I could not find any documentation about the ‘yokogawa’-convention (which is probably the reason why the yokogawa-entry in the table on <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>
is empty). Perhaps one of the Yokogawa-users on this list could chime in to enlighten you, or you could check the system’s documentation to find out what the expected.</div>
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<div class="">The easy solution would be to register the mri to an RAS-based coordinate system (e.g. use cfg.coordsys = ’neuromag’ for ft_volumerealign), but I would recommend to get to the bottom of this, and provide a principled solution. Once you have found
out about the conventional coordinate system for yokogawa systems, it would be great if you could update the table on (<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>).
Note, that if it turns out to be that there is no specific convention (e.g. site-specific ALS or RAS or so) it is worth documenting, too.</div>
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<div class="">Good luck</div>
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<div class="">Jan-Mathijs</div>
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<div class="">J.M.Schoffelen<br class="">
Senior Researcher<br class="">
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br class="">
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<div class="">On 19 Oct 2016, at 08:02, Susmita Sen <<a href="mailto:susmitasen.ece@gmail.com" class="">susmitasen.ece@gmail.com</a>> wrote:</div>
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<div style="font-size:large" class=""><span style="font-size:12.8px" class="">Dear FieldTrip community,</span><br clear="all" class="">
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<div class=""><span style="font-size:12.8px" class="">I am constructing headmodel using standard mri data. The meg data that I am working with is recorded using yokogawa system. I have used the following code.</span></div>
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<div class=""><font face="monospace, monospace" class="">load('standard_mri.mat')</font></div>
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<div class=""><font face="monospace, monospace" class="">cfg = [];</font></div>
<div class=""><span style="font-family:monospace,monospace" class="">cfg.coordsys = 'yokogawa';</span><br class="">
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<div class=""><font face="monospace, monospace" class="">cfg.viewresult = 'yes';</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.snapshot = 'yes';</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.fiducial.nas = mri.hdr.fiducial.mri.nas; %position of nasion</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.fiducial.lpa = mri.hdr.fiducial.mri.lpa; %position of LPA</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.fiducial.rpa = mri.hdr.fiducial.mri.rpa; %position of RPA</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.fiducial.zpoint = [ 91 109 107];</font></div>
<div class=""><font face="monospace, monospace" class="">[mri_realigned] = ft_volumerealign(cfg,mri);</font></div>
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<div class=""><span style="font-family:monospace,monospace" class="">%% SEGMENTATION</span><br class="">
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<div class=""><font face="monospace, monospace" class="">cfg = [];</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.output = 'brain';</font></div>
<div class=""><font face="monospace, monospace" class="">segmentedmri = ft_volumesegment(cfg, mri_realigned);</font></div>
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<div class=""><font face="monospace, monospace" class="">%% create headmodel</font></div>
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<div class=""><span style="font-family:monospace,monospace" class="">cfg = [];</span><br class="">
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<div class=""><font face="monospace, monospace" class="">cfg.method='singleshell';</font></div>
<div class=""><font face="monospace, monospace" class="">vol = ft_prepare_headmodel(cfg, segmentedmri);</font></div>
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<div class=""><font face="monospace, monospace" class="">%% visualize </font></div>
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<div class=""><span style="font-family:monospace,monospace" class="">vol = ft_convert_units(vol,'cm');</span><br class="">
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<div class=""><font face="monospace, monospace" class="">grad = ft_read_sens('D:\Data\all\raw_preproc_data\raw\ari.con'); % load grad</font></div>
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<div class=""><font face="monospace, monospace" class="">figure</font></div>
<div class=""><font face="monospace, monospace" class="">ft_plot_sens(grad, 'style', '*b');</font></div>
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<div class=""><font face="monospace, monospace" class="">hold on</font></div>
<div class=""><font face="monospace, monospace" class="">ft_plot_vol(vol);</font></div>
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<div class="">However, I am facing a problem when I plotting headmodel with the sensors. I noticed that the orienations of headmodel and sensors are not aligned. I am attaching the figure with this mail. I would be very greatful if any could kindly give me
suggestions how to align these two. </div>
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<div class=""><span id="cid:ii_157db81e9d700ba3"><Headmodel_sens1.jpg></span><br class="">
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<div class=""><span id="cid:ii_157db82deba0e43b"><Headmodel_sens2.jpg></span><br class="">
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<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>
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