[FieldTrip] Orientation of headmodel with respect to sensors poisition

[Susmita Sen]

Thanks a lot.

Thanks and Regards,
Susmita Sen
Research Scholar
Audio and Bio Signal Processing Lab.
E & ECE Dept.
IIT Kharagpur

On Wed, Oct 19, 2016 at 12:45 PM, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:

> Dear Susmita,
>
> 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 http://www.
> fieldtriptoolbox.org/faq/how_are_the_different_head_and_
> mri_coordinate_systems_defined 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.
>
> 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 (
> http://www.fieldtriptoolbox.org/faq/how_are_the_different_
> head_and_mri_coordinate_systems_defined). 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.
>
> Good luck
>
> Jan-Mathijs
>
> J.M.Schoffelen
> Senior Researcher
> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands
>
>
>
>
> On 19 Oct 2016, at 08:02, Susmita Sen <susmitasen.ece at gmail.com> wrote:
>
> Dear FieldTrip community,
>
> 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.
>
>
> load('standard_mri.mat')
>
> cfg = [];
> cfg.coordsys = 'yokogawa';
> cfg.viewresult = 'yes';
> cfg.snapshot     = 'yes';
> cfg.fiducial.nas    = mri.hdr.fiducial.mri.nas; %position of nasion
> cfg.fiducial.lpa    = mri.hdr.fiducial.mri.lpa; %position of LPA
> cfg.fiducial.rpa    = mri.hdr.fiducial.mri.rpa; %position of RPA
> cfg.fiducial.zpoint =  [ 91 109 107];
> [mri_realigned] = ft_volumerealign(cfg,mri);
>
> %% SEGMENTATION
>
> cfg           = [];
> cfg.output    = 'brain';
> segmentedmri  = ft_volumesegment(cfg, mri_realigned);
>
> %% create headmodel
>
> cfg = [];
> cfg.method='singleshell';
> vol = ft_prepare_headmodel(cfg, segmentedmri);
>
> %% visualize
>
> vol = ft_convert_units(vol,'cm');
> grad = ft_read_sens('D:\Data\all\raw_preproc_data\raw\ari.con'); % load
> grad
>
> figure
> ft_plot_sens(grad, 'style', '*b');
>
> hold on
> ft_plot_vol(vol);
>
> 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.
>
> <Headmodel_sens1.jpg>
>
> <Headmodel_sens2.jpg>
>
>
> Thanks and Regards,
> Susmita Sen
> Research Scholar
> Audio and Bio Signal Processing Lab.
> E & ECE Dept.
> IIT Kharagpur
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