%%% MCINET BASC script for regular grid of resolutions/scales

clear all

addpath(genpath('/home/atam/quarantaine/niak-boss-0.12.18'));

path_data = '/home/atam/database/';

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Setting input/output files %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

files_in = niak_grab_region_growing([path_data 'adnet/region_growing_20141210/rois/']);
files_in.infos = [path_data 'adnet/models/admci_model_group_20141210.csv']; % A file of comma-separeted values describing additional information on the subjects, this can be omitted

%%%%%%%%%%%%%
%% Options %%
%%%%%%%%%%%%% 

opt.folder_out = [path_data 'adnet/basc_40sc_20141210/']; % Where to store the results
opt.grid_scales = 5:5:200; % Search for stable clusters in the range 5 to 200
% opt.scales_maps = repmat(opt.grid_scales,[1 3]); % The scales that will be used to generate the maps of brain clusters and stability. 
%                                                  % In this example the same number of clusters are used at the individual (first column), 
%                                                  % group (second column) and consensus (third and last colum) levels.
opt.scales_maps = [5 5 5;...
10 10 10;...
15 15 15;...
20 20 20;...
25 25 25;...
30 30 30;...
35 35 35;...
40 40 40;...
45 45 45;...
50 50 50;...
55 55 55;...
60 60 60;...
65 65 65;...
70 70 70;...
75 75 75;...
80 80 80;...
85 85 85;...
90 90 90;...
95 95 95;...
100 100 100;...
105 105 105;...
110 110 110;...
115 115 115;...
120 120 120;...
125 125 125;...
130 130 130;...
135 135 135;...
140 140 140;...
145 145 145;...
150 150 150;...
155 155 155;...
160 160 160;...
165 165 165;...
170 170 170;...
175 175 175;...
180 180 180;...
185 185 185;...
190 190 190;...
195 195 195;...
200 200 200];
opt.stability_tseries.nb_samps = 100; % Number of bootstrap samples at the individual level. 100: the CI on indidividual stability is +/-0.1
opt.stability_group.nb_samps = 1000; % Number of bootstrap samples at the group level. 500: the CI on group stability is +/-0.05

opt.flag_ind = false;   % Generate maps/time series at the individual level
opt.flag_mixed = false; % Generate maps/time series at the mixed level (group-level networks mixed with individual stability matrices).
opt.flag_group = true;  % Generate maps/time series at the group level

%%%%%%%%%%%%%%%%%%%%%%
%% Run the pipeline %%
%%%%%%%%%%%%%%%%%%%%%%
opt.flag_test = false; % Put this flag to true to just generate the pipeline without running it. Otherwise the region growing will start. 
opt.psom.qsub_options= '-A gsf-624-aa -q sw -l nodes=1:ppn=2 -l walltime=30:00:00';
%opt.psom.max_queued = 10; % Uncomment and change this parameter to set the number of parallel threads used to run the pipeline
pipeline = niak_pipeline_stability_rest(files_in,opt);