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Seizure-Waves-Validation

Notes

Usage

Generate simulations

Use the SCM class to make a seizing cortical model simulation. There are lots of options in here, but what's shown below will generate the simulations with the same parameters from Figure 1 of REF.

The property base_dir controls where the simulations are saved. The default behavior is to save everything in a folder called 'SCM' in the current working directory (~/SCM). The full state of the simulation is saved at 1 s intervals in files with names like

~/SCM/LABEL/LABEL_NN_TTT.mat

where NN represents the simulation number (SCM.sim_num) and TTT is the starting time of the segment. The simulated MEA data (the small subregion of the simulation that mimics an MEA recording) is saved to

~/SCM/LABEL_SeizureNN_MEA_PP_PP.mat

where PP indicates the duration of the pre- and post-ictal periods (SCM.padding). In both naming schemes, LABEL is any string value (SCM.label).

Figure 1A: A fixed source simulation (no ictal wavefront)

scm = SCM('FS');

% Use the following to see where the outputs will be saved:
disp(scm.basename);
disp(scm.mea_path);

% Start the simulation
scm.Run();

Figure 1E: A simulation where the fixed source location shifts midway through the seizure

% Create a fixed source simulation. Results will be saved to
% folders 'SCM' (full state of sim) and 'FS' (MEA)
scm = SCM('SW');
scm.Run();
Some other methods
  • show_layout(): Show the simulation layout (locations of the irritative zone, fixed sources, MEA, and IW source)
  • rotate(theta): Rotate the locations of fixed and IW sources by angle theta about the center of the simulation
  • Preview(show_layout=false): Generates a set of figures with panels showing excitatory firing rates (Qe) and potassium (K) states at each save point (defaults to every 1 second; controlled by parameter t_step)

Load MEA data

Assumes that the MEA data is stored in a .mat file with the following fields:

BadChannels                 18x1                        144  double              
Data                   1875001x96                 360000192  int16               
Duration                     1x1                          8  double              
Map                         10x10                       800  double              
Padding                      1x2                         16  double              
Patient                      1x2                          4  char                
Position                    96x2                       1536  double              
SamplingRate                 1x1                          8  double              
Seizure                      1x1                          2  char                
Time                         1x1875001              7500004  single              

mea = MEA(<path_to_mea_file>);

Identify ictal wavefronts

iw = mea.IW();
iw.plot()
iw.plot2D()

Estimate traveling wave directions

The following will save the wave direction estimates to a folder called WaveFits in your current directory (~/WaveFits). The D-method can take a long time to run, so we have provided a helper script (d10_helper.m) that runs the analysis in segments. This allows you to pick up where you left off if your run is interrupted. To do so, simply keep re-running d10_helper; (with the same mea data) until the analysis is complete.

mea = MEA(<path_to_mea_file>);
s = mkdir(['WaveFits/' mea.Name]);

% M-method direction estimatees
times = mea.get_discharge_times('lfp_cross');
M = mea.max_descent(times, 'halfwin', 0.05);
save(fullfile('WaveFits', mea.Name, 'M'), 'M');

% D-method direction estimates
% This method is slow so we recommend using the helper script (shown below)
step = 0.1;
times = mea.Time(1):step:mea.Time(end);
D = mea.delays(times, ...
        'halfwin', 5, 'fband', [1 13], 'minfreq', 3);
save(fullfile('WaveFits', mea.Name, 'D'), 'D');

% D-method alternative
d10_helper;
  % if this is interrupted, reinstantiate `mea` and run `d10_helper` again.

Identify intervals with stable traveling wave directions

% Load pre-saved discharge arrival times
M = load('WaveFits/P1_Seizure1/M.mat').M;
intervals = M.stable_intervals();
scatter(intervals.time, intervals.dir_trend, [], intervals.phase_num);