[FieldTrip] Orientation of headmodel with respect to sensors poisition

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Wed Oct 19 09:15:34 CEST 2016

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


Senior Researcher
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands

On 19 Oct 2016, at 08:02, Susmita Sen <susmitasen.ece at gmail.com<mailto: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.


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);


cfg           = [];
cfg.output    = 'brain';
segmentedmri  = ft_volumesegment(cfg, mri_realigned);

%% create headmodel

cfg = [];
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

ft_plot_sens(grad, 'style', '*b');

hold on

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.



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