Releases: lrkrol/SEREEGA
SEREEGA v1.5.0
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.
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.
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
SEREEGA v1.2.2
These patches update some documentation that was overlooked for release v1.2.0.
Changelog since v.1.2.0:
v1.2.2
- Fixed forgotten version increment in eegplugin_sereega.m
- Fixed forgotten documentation update reflecting 2018-06-04 utl_apply_dvslopeshift change
SEREEGA v1.2.0
Introduced parallel processing to speed up simulation whenever the Parallel Computing toolbox is available, with minor accompanying changes as well as minor additions/fixes.
Changelog since v.1.1.0:
v1.2.0
- Added text to plot_component_signal plot indicating number of averages taken
- Added utl_add_markers_toeeglabdataset following GitHub issue #13
- Fixed typo in BioSemi-32 montage in utl_get_montage
- Switched to parallel processing in generate_scalpdata where available, following GitHub issue #14, also adding utl_show_progress_parfor and utl_show_progress_timetocomplete to replace progress bar
SEREEGA v1.1.0
legacy_rndmultsrc argument of generate_scalpdata.
SEREEGA is out of beta since no new issues have been reported in over a year.
Changelog since v1.0.19-beta:
v1.1.0
- Added electrodes argument to plot_source_projection
- Added lf_prune_nyheadfile to reduce NY Head lead field filesize
- Changed generate_scalpdata behaviour when one component has multiple sources. The projections from each source are now summed together. Previous behaviour, which used only one randomly chosen souce per epoch, can be reinstated with the argument legacy_rndmultsrc.
SEREEGA v1.0.19-beta
A number of bugfixes and improvements, primaily based on received feedback and reported issues. SEREEGA has been successfully used by a number of labs by now, but assuming that some additional issues may yet be caught, I'm leaving it in beta for just a little longer.
Changelog since v1.0.11-beta:
v1.0.19-beta
- Lead fields now continue with empty labels (i.e. all channels) if montage not found
- Fixed bug in utl_shift_latency arguments
- Added utl_apply_dvslopeshift, and replaced all calls to predecessor utl_apply_dvslope with it
- Added utl_multigradient for updated default projection colormap
- Added utl_epoch2continuous after GitHub issue #4
- Fixed GitHub issue #10 where latencies were off by 1 sample in erp_generate_signal and ersp_generate_signal
- Added shading argument to plot_source_projection
- Fixed GitHub issue #11 where utl_multigradient was not called in plot_source_projection and plot_component_projection
SEREEGA v1.0.11-beta
Mostly GUI improvements, as this is the first release to be made available in EEGLAB through the plug-in manager.
This is also the first release since the SEREEGA manuscript's official journal publication. See: Krol, L. R., Pawlitzki, J., Lotte, F., Gramann, K., & Zander, T. O. (2018). SEREEGA: Simulating Event-Related EEG Activity. Journal of Neuroscience Methods, 309, 13-24.
Changelog since v1.0.5-beta:
v1.0.11-beta
- Fixed GitHub issue #3 in lf_get_projection
- Fixed issue in pop_sereega_plot_headmodel
- Improved feedback for some pop_ functions
- Made the menu available in EEGLAB even when no dataset is loaded
- Added utl_isvalidcomponent
- Fixed GUI issue in plot_source_location
SEREEGA v1.0.5-beta
This is the version described in Krol, L. R., Pawlitzki, J., Lotte, F., Gramann, K., & Zander, T. O. (2018). SEREEGA: Simulating Event-Related EEG Activity. bioRxiv doi: 10.1101/326066, with slight patches.
Changelog:
v1.0.5-beta
- Updated GUI with previous version's changes
v1.0.4-beta
- Added peakLatencyShift parameter to ERP class
- Added frequencyShift parameter to ERSP class
- Updated ERSP classes in utl_get_component_fromtemplate using frequencyShift
- Fixed utl_apply_dvslope to never apply deviations exceeding indicated deviation value
v1.0.0-beta
- The version described in and used for the bioRxiv preprint 326066
SEREEGA v1.0.0-beta
This is the version described in and used for Krol, L. R., Pawlitzki, J., Lotte, F., Gramann, K., & Zander, T. O. (2018). SEREEGA: Simulating Event-Related EEG Activity. bioRxiv doi: 10.1101/326066.