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updated tags, see fieldtrip#810
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robertoostenveld authored and schoffelen committed Nov 26, 2024
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2 changes: 1 addition & 1 deletion example/bids.md
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---
title: BIDS - the brain imaging data structure
tags: [bids, sharing]
tags: [example, bids, sharing]
---

# BIDS - the brain imaging data structure
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4 changes: 2 additions & 2 deletions example/neuromag_aligned2mni.md
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title: Read neuromag .fif mri and create a MNI-aligned single-shell head model
---

# Read neuromag .fif mri and create a MNI-aligned single-shell head model

{% include markup/red %}
The below example code is hopelessly outdated (thus deprecated) and will probably not work anymore. This page is kept in place just for reference. If you ended up on this page because you are curious to learn about the creation of dipole grids from .fif MRI, please look at [this](/example/sourcemodel_aligned2mni) example script.
{% include markup/end %}

# Read neuromag .fif mri and create a MNI-aligned single-shell head model

This example script is derived from the example script [Create MNI-aligned grids in individual head_space](/example/sourcemodel_aligned2mni). But for Neuromag data there are some differences. First make a MNI template as is done in the above mentioned example script.

%==================================================================
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6 changes: 2 additions & 4 deletions example/planar_orientation.md
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---
title: Find the orientation of planar gradiometers
tags: [neuromag, planar]
tags: [example, neuromag, planar]
---

# Find the orientation of planar gradiometers

The Neuromag/Elekta/Megin Vectorview and Triux scanners have a combination of magnetometers and two planar gradiometers at each sensor location.

This is further detailed in the Neuromag/Elekta/MEGIN System Hardware Users' Guide and on [this page](http://imaging.mrc-cbu.cam.ac.uk/meg/VectorviewDescription#Magsgrads).
The Neuromag/Elekta/Megin Vectorview and Triux scanners have a combination of magnetometers and two planar gradiometers at each sensor location. This is detailed in the Neuromag/Elekta/MEGIN System Hardware Users' Guide and on [this page](http://imaging.mrc-cbu.cam.ac.uk/meg/VectorviewDescription#Magsgrads).

The following code demonstrates how you can determine the orientation of the two planar channels at each location.

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11 changes: 6 additions & 5 deletions example/sphere_fitting.md
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---
title: Fitting a template MRI to the MEG Polhemus head shape
tags: [example, headmodel, meg]
redirect_from:
- /example/sphere_fitting_and_scaling_of_the_template_colin_27_mri_to_the_meg_polhemus_headshape/
---
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load standard_mri % Colin 27 template in fieldtrip

% read MEG sensor location
MEG_sens = ft_read_sens(dataset, 'senstype', 'meg');
MEG_sens = ft_convert_units(MEG_sens, 'mm');
grad = ft_read_sens(dataset, 'senstype', 'meg');
grad = ft_convert_units(grad, 'mm');

% read polhemus headshape
headshape = ft_read_headshape(dataset);
headshape = ft_convert_units(headshape, 'mm');

save headshape headshape
save MEG_sens MEG_sens
save grad grad

% realign to neuromag coordinate system
lpa = [ 7 104 26];
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cfg.fiducial.rpa = rpa;
cfg.fiducial.zpoint = zpoint;
cfg.coordsys = 'neuromag';
mri_realigned_fiducial = ft_volumerealign(cfg,mri);
mri_realigned_fiducial = ft_volumerealign(cfg,mri);

cfg = [];
cfg.output = {'brain','skull','scalp'};
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brain_scaled = ft_prepare_mesh(cfg, segmentedmri);

figure
%ft_plot_sens(MEG_sens, 'style', '*b');
% ft_plot_sens(grad, 'style', '*b');
ft_plot_headshape(headshape_denosed);
hold on
ft_plot_mesh(scalp_scaled, 'edgecolor', 'none', 'facecolor', [1 1 1]/1.2, 'facealpha', 0.5)
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