simlayer_free_energy_patch_size.m

function simlayer_free_energy_patch_size(subj_info, session_num, invfoi,...
    SNR, varargin)
% SIMLAYER_FREE_ENERGY_PATCH_SIZE  Run simulations with whole brain - free energy
%   analysis, with multiple simulate/reconstruct patch size combinations
%
% Use as
%   simlayer_free_energy_patch_size(subjects(1), 1, [10 30], -20)
% where the first argument is the subject info structure (from create_subjects),
% the second is the session number, the third is the frequency range, and
% the fourth is the SNR (db).
% 
%   simlayer_free_energy_patch_size(...,'param','value','param','value'...) allows
%    additional param/value pairs to be used. Allowed parameters:
%    * surf_dir - directory containing subject surfaces
%    * mri_dir - directory containing subject MRIs
%    * out_file - output file name (automatically generated if not
%    specified)
%    * dipole_moment - 10 (default) or interger - moment of simulated
%    dipole
%    * nsims - 60 (default) or integer - number of simulations per surface

% Parse inputs
defaults = struct('surf_dir', 'd:\pred_coding\surf', 'mri_dir', 'd:\pred_coding\mri',...
    'dipole_moment', 10, 'nsims', 60);  %define default values
params = struct(varargin{:});
for f = fieldnames(defaults)',
    if ~isfield(params, f{1}),
        params.(f{1}) = defaults.(f{1});
    end
end

spm('defaults', 'EEG');
spm_jobman('initcfg'); 

patch_sizes=[5 10];

for sp=1:length(patch_sizes)
    sim_patch_size=patch_sizes(sp);
    for rp=1:length(patch_sizes)
        reconstruct_patch_size=patch_sizes(rp);

        out_file=sprintf('allcrossF_f%d_%d_SNR%d_dipolemoment%d_sim%d_reconstruct%d.mat',...
            invfoi(1),invfoi(2),SNR,params.dipole_moment,sim_patch_size,...
            reconstruct_patch_size);

        simlayer_free_energy(subj_info, session_num, invfoi, SNR,...
            'surf_dir', params.surf_dir, 'mri_dir', params.mri_dir,...
            'out_file', out_file, 'dipole_moment', params.dipole_moment,...
            'sim_patch_size', sim_patch_size, 'reconstruct_patch_size',...
            reconstruct_patch_size, 'nsims', params.nsims);

    end
end