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Improve support for yokogawa (and possible future OPM systems) #819

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34 changes: 18 additions & 16 deletions getting_started/yokogawa.md
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Expand Up @@ -295,29 +295,31 @@ Using the MRI fiducial positions expressed in [head coordinates](/faq/coordsys),
Alternative to reading the gradiometer definition from the raw data file, you can also obtain the gradiometer definition after **[ft_preprocessing](/reference/ft_preprocessing)**, **[ft_timelockanalysis](/reference/ft_timelockanalysis)** or **[ft_freqanalysis](/reference/ft_freqanalysis)**: the data structures resulting from those functions contain the "grad" field which corresponds to the gradiometer definition from the original raw file.

% add the fiducials (expressed in dewar coordinates) to the gradiometer definition
grad.fid.pnt(1,:) = fid1_dewarcoordinates;
grad.fid.pnt(2,:) = fid2_dewarcoordinates;
grad.fid.pnt(3,:) = fid3_dewarcoordinates;
grad.fid.pos(1,:) = fid1_dewarcoordinates;
grad.fid.pos(2,:) = fid2_dewarcoordinates;
grad.fid.pos(3,:) = fid3_dewarcoordinates;

grad.fid.label{1} = 'fid1_label';
grad.fid.label{2} = 'fid2_label';
grad.fid.label{3} = 'fid3_label';

target.fid.pos(1,:) = fid1_headcoordinates;
target.fid.pos(2,:) = fid1_headcoordinates;
target.fid.pos(3,:) = fid1_headcoordinates;

target.fid.label{1} = 'fid1_label';
target.fid.label{2} = 'fid2_label';
target.fid.label{3} = 'fid3_label';

% the configuration for FT_SENSORREALIGN should specify the three fiducials in
% head coordinates as obtained from the aligned MRI using FT_SOURCEPLOT
cfg = [];
cfg.method = 'fiducial';
cfg.template.pnt = [
fid1_headcoordinates
fid2_headcoordinates
fid3_headcoordinates
];
cfg.template.label = {
'fid1_label'
'fid2_label'
'fid3_label'
};
grad_aligned = ft_sensorrealign(cfg, grad);
cfg.method = 'template';
cfg.target = target.fid;
cfg.elec = grad.fid;
grad_aligned = ft_electroderealign(cfg);

grad_head = ft_transform_geometry(grad_aligned.rigidbody, grad, 'rigidbody');

## Example: Sourceanalysis

Expand Down Expand Up @@ -541,4 +543,4 @@ Thanks to Akiko Ikkai for contributing her data for making this page.

## See also

{% include seealso tag="yokogawa" %}
{% include seealso tag="yokogawa" %}
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