fit_model.m

function [] = fit_model(alpha_v, alpha_f, lambda_1, lambda_2, outpath)

if isdeployed
    %command line arguments are passed in as string
    alpha_v = str2num(alpha_v)
    alpha_f = str2num(alpha_f)
    lambda_1 = str2num(lambda_1)
    lambda_2 = str2num(lambda_2)
else
    disp('loading paths')

    %for matlab2
    addpath(genpath('/home/hayashis/git/encode-dp')); 
    addpath(genpath('/home/hayashis/git/vistasoft'));
    addpath(genpath('/home/hayashis/git/jsonlab'));

    %for hpc
    addpath(genpath('/N/u/brlife/git/encode-dp'));
    addpath(genpath('/N/u/brlife/git/vistasoft'));
    addpath(genpath('/N/u/brlife/git/jsonlab'));
end

taskid = getenv('SLURM_ARRAY_TASK_ID')
config = loadjson('config.json')

disp('loading dt6.mat')
dt6 = loadjson(fullfile(config.dtiinit, 'dt6.json'))
aligned_dwi = fullfile(config.dtiinit, dt6.files.alignedDwRaw)

%need to use different profile directory to make sure multiple jobs won't share the same directory and crash
profile_dir=fullfile('./profile', int2str(feature('getpid')));
mkdir(profile_dir);
c = parcluster();
c.JobStorageLocation = profile_dir;
pool = parpool(c, config.workers);

%rng(sum(100*clock)); % seed used for random selection of voxels (same seed for same experiment)

disp([ 'alpha_v=', num2str(alpha_v), ...
       ' alpha_f=', num2str(alpha_f), ...
       ' lambda_1=', num2str(lambda_1), ...
       ' lambda_2=', num2str(lambda_2)])

[~, results] = FitFullModelSampleVoxels_and_Fibers(...
    aligned_dwi, ...
    config.track, ...
    'bogus', ...
    config.L, ...
    config.p, ...
    config.n, ...
    config.m, ...
	alpha_v, ...
	alpha_f, ...
	lambda_1, ...
	lambda_2, ...
	config.afq);

%save results
%fileName = fullfile('results', strcat('alpha_v_',num2str(alpha_v),'_alpha_f_',num2str(0), '_lambda_1_',num2str(lambda_1),'_lambda_2_',num2str(lambda_2),'.mat'));
save(outpath, 'results')

delete(pool);