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Added atlas support, HArtMuT
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@lrkrol
lrkrol committed Dec 8, 2022
1 parent 06d9e15 commit 08b83bd
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5 changes: 4 additions & 1 deletion .gitignore
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*to*_Atlas_v2/
HArtMuT_mix_Colin27_small.mat
HArtMuT_NYhead_small.mat
mni2atlas/
sa_nyhead.mat
sa_nyhead_sereegareduced.mat
*.asv
*.asv
*.afdesign
197 changes: 122 additions & 75 deletions docs/README.md
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10 changes: 10 additions & 0 deletions docs/changelog.txt
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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

v1.2.2
- Fixed forgotten version increment in eegplugin_sereega.m
- Fixed forgotten documentation update reflecting 2018-06-04 utl_apply_dvslopeshift change
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10 changes: 7 additions & 3 deletions eegplugin_sereega.m
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% Team PhyPA, Biological Psychology and Neuroergonomics,
% Berlin Institute of Technology

% 2022-11-17 lrk
% - Added HArtMuT lead field
% 2018 through 2021 lrk
% - Version number increments
% 2018-04-23 First version
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function version = eegplugin_sereega(fig, try_strings, catch_strings)

version = '1.2.0';
version = '1.5.0';

% find tools menu
% ---------------
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'eeglab redraw;' ...
];
cb_epochs = 'EEG = pop_sereega_epochs(EEG);';
cb_lf_fieldtrip = 'EEG = pop_sereega_lf_generate_fromfieldtrip(EEG);';
cb_lf_hartmut = 'EEG = pop_sereega_lf_generate_fromhartmut(EEG);';
cb_lf_nyhead = 'EEG = pop_sereega_lf_generate_fromnyhead(EEG);';
cb_lf_pha = 'EEG = pop_sereega_lf_generate_frompha(EEG);';
cb_lf_fieldtrip = 'EEG = pop_sereega_lf_generate_fromfieldtrip(EEG);';
cb_comp_sources = 'EEG = pop_sereega_sources(EEG);';
cb_comp_signals = 'EEG = pop_sereega_signals(EEG);';
cb_comp_components = 'EEG = pop_sereega_components(EEG);';
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menu_new = uimenu(menu_root, 'label', 'New empty dataset', 'userdata', userdata, 'callback', cb_new);
menu_epochs = uimenu(menu_root, 'label', 'Configure epochs', 'userdata', userdata, 'callback', cb_epochs);
menu_lf = uimenu(menu_root, 'label', 'Configure lead field');
menu_lf_fieldtrip = uimenu(menu_lf, 'label', 'FieldTrip', 'userdata', userdata, 'callback', cb_lf_fieldtrip);
menu_lf_hartmut = uimenu(menu_lf, 'label', 'HArtMuT', 'userdata', userdata, 'callback', cb_lf_hartmut);
menu_lf_nyhead = uimenu(menu_lf, 'label', 'New York Head', 'userdata', userdata, 'callback', cb_lf_nyhead);
menu_lf_pha = uimenu(menu_lf, 'label', 'Pediatric Head Atlas', 'userdata', userdata, 'callback', cb_lf_pha);
menu_lf_fieldtrip = uimenu(menu_lf, 'label', 'FieldTrip', 'userdata', userdata, 'callback', cb_lf_fieldtrip);
menu_comp = uimenu(menu_root, 'label', 'Configure components', 'userdata', userdata);
menu_comp_sources = uimenu(menu_comp, 'label', 'Select source locations', 'userdata', userdata, 'callback', cb_comp_sources);
menu_comp_signals = uimenu(menu_comp, 'label', 'Define signal activations', 'userdata', userdata, 'callback', cb_comp_signals);
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6 changes: 6 additions & 0 deletions leadfield/fieldtrip/lf_generate_fromfieldtrip.m
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% for each source.
% .pos - xyz MNI coordinates of each source
% .chanlocs - channel information in EEGLAB format
% .atlas - atlas (region) indication for each source; this
% is simply 'Brain' until more specific
% functionality is added
%
% Usage example:
% >> lf = lf_generate_fromfieldtrip('labels', {'Fz', 'Cz', 'Pz'}, ...
Expand All @@ -40,6 +43,8 @@
% Team PhyPA, Biological Psychology and Neuroergonomics,
% Berlin Institute of Technology

% 2021-01-06 lrk
% - Added lf.atlas
% 2018-11-08 lrk
% - Now continues with empty labels if montage not found
% 2018-03-26 lrk
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lf.pos = ftlf.pos(ftlf.inside,:);
lf.chanlocs = readlocs('chanlocs-standard_1005.elp');
lf.chanlocs = lf.chanlocs(chanidx);
lf.atlas = repmat({'Brain'}, size(lf.pos, 1), 1);

end
231 changes: 231 additions & 0 deletions leadfield/hartmut/chanlocs-hartmut-NYhead_small.xyz
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