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SEREEGA v1.5.0

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@lrkrol lrkrol released this 09 Dec 12:25
· 3 commits to master since this release
v1.5.0
c469ba7

This release introduces a number of significant new features. It adds

  • atlas support,
  • two new head models from the recently-released HArtMuT family, as well as the ability to use
  • custom head models created in Brainstorm.

Atlas support means that sources can now be obtained by indicating specific regions in the brain, rather than coordinates. Atlases are available for the recently updated New York Head and the newly added HArtMuT models; Brainstorm also supports atlases. Atlases for older head models can be added post hoc, albeit with varying success, using mni2atlas which is supported via lf_add_atlas_frommni2atlas (but note the more restrictive licence).

As an example using the New York Head and associated atlas, the following figure inspects a source in one particular, named region using the provided SEREEGA code.

SEREEGA atlas support

Code for above figure 
lf = lf_generate_fromnyhead();
region = {'Brain_Right_Temporal_Pole'};

figure;
subplot(1,3,1)
    plot_source_location(lf_get_source_all(lf, 'region', region), lf, 'mode', '3d', 'view', [140 20], 'newfig', 0);
    title(region, 'Interpreter', 'none');
    axis tight;
subplot(1,3,2)
    plot_headmodel(lf, 'region', region, 'electrodes', 0, 'view', [140 20], 'newfig', 0);
    plot_source_moment(lf_get_source_middle(lf, 'region', region), lf, 'scale', 25);
    title('middle source moment');
    axis tight;
subplot(1,3,3)
    plot_source_projection(lf_get_source_middle(lf, 'region', region), lf, 'orientedonly', 1, 'newfig', 0);

The HArtMuT head models include sources representing eyes, facial muscles, and dorsal neck muscles, on top of cortical sources. The following figure, for example, shows the location, moment, and projection of two sources from the middle of the left and right corneas.

SEREEGA HArtMuT support

Code for above figure 
lf = lf_generate_fromhartmut('NYhead_small');

sourceIdx = [lf_get_source_middle(lf, 'region', {'EyeCornea_left_vertical'}), ...
             lf_get_source_middle(lf, 'region', {'EyeCornea_right_vertical'})];

figure;
subplot(1,2,1);
    plot_headmodel(lf, 'labels', 0, 'view', [150 20], 'newfig', 0);
    plot_source_moment(sourceIdx, lf);
    axis tight;
subplot(1,2,2);
    plot_source_projection(sourceIdx, lf, 'orientedonly', 1, 'newfig', 0);

(Note that the eye dipoles here are oriented in the direction of movement, not the direction of gaze.)

Furthermore, the newly added lf_generate_frombrainstorm allows custom lead fields generated in Brainstorm to be used in SEREEGA. This makes a host of personalised lead fields available.

Additional changes include the plot_source_moment function also demonstrated above, and the utl_call_gui function which gives command-line access to GUI features, such as the pop_sereega_sources dialog, which has no easy scripted equivalent.

Changelog since v1.2.2:

v1.5.0

  • Added utl_call_gui, allowing GUI functions to be called without requiring the EEGLAB GUI itself to be used or a SEREEGA dataset to be loaded
  • Added source ID to pop_sereega_sources GUI and console output
  • Various documentation updates
  • Added support for new HArtMuT (Head Artefact Model using Tripoles) head models containing ocular and muscular sources alongside brain sources
  • Added atlas support, allowing sources to be selected from specified named regions. SEREEGA leadfields now have an additional atlas field containing, for each source, the name of the region it belongs to. lf_get_source_* functions have been added/adjusted to allow sources to be obtained from specific regions. lf_add_atlas_frommni2atlas can be used to add atlases to existing lead fields using the mni2atlas function from the FMRIB Software Library (not included).
  • Added electrodes argument to plot_headmodel
  • Added plot_source_moment to plot source orientation as arrow
  • Added support for lead fields generated in Brainstorm
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