Actigraphy_Stats_v2_1.m

function Actigraphy_Stats_v2_1(segment)

%clc
%clear all
%close all

path_code = '/home/aldo/Documents/Projects/Avtivemeter/Data';

if(strcmp(segment,'morning'))
    path_control = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/Controls/';
    path_lis = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/LIS/';
    path_emcs = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/EMCS/';
    path_mcs_p = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/MCS+/';
    path_mcs_m = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/MCS-/';
    path_mcs_ast = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/MCS_ast/';
    path_mcs = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/MCS/';
    path_uws = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/UWS/';
    path_uws_ast = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/UWS_ast/';
    path_uws_non_TBI = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/UWS/NonTBI/';
    path_uws_TBI = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/UWS/TBI/';

elseif(strcmp(segment,'mtn_files'))
    path_control = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/healthy_control/';
    path_emcs = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/EMCS/';
    path_mcs_p = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/MCS+/';
    path_mcs_m = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/MCS-/';
    path_mcs_ast = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/MCS_ast/';
    path_mcs = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/MCS/';
    path_uws = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/UWS/';
    path_lis = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/LIS/';
  %  path_uws_non_TBI = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/UWS/NonTBI/';
  %  path_uws_TBI = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/UWS/TBI/';

elseif(strcmp(segment,'night'))
    path_control = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Nights/Controls/';
    path_emcs = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Nights/EMCS/';
    path_mcs_p = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Nights/MCS+/';
    path_mcs_m = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Nights/MCS-/';
    path_mcs_ast = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Nights/MCS*/';
    path_mcs = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Nights/MCS/';
    path_uws = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Nights/UWS/';
    path_uws_ast = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Nights/UWS*/';

elseif(strcmp(segment,'allday'))
    path_control = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/All_day/Controls/';
    path_emcs = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/All_day/EMCS/';
    path_mcs_p = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/All_day/MCS+/';
    path_mcs_m = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/All_day/MCS-/';
    path_mcs_ast = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/All_day/MCS*/';
    path_mcs = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/All_day/MCS/';
    path_uws = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/All_day/UWS/';
    path_uws_ast = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/All_day/UWS*/';
    
else
      fprintf(1,'\n I do not recognize that segment sorry \n' )
end
%%%%%% Import data for Group 1: Controls


cd(path_control);
SUBJlist_Control = dir('*.mat');

for i = 1:length(SUBJlist_Control)
    SUBJname_Control = SUBJlist_Control(i).name;
%     path1=([path SUBJname]);
%     cd(path1);
    data=load(SUBJname_Control);
    Control_aux(i,:,:) = data.aux;
end
t_control = data.time;
% figure
% plot(t_control, Control_aux');


%%%%%% Import data for Group 2: EMCSs

cd(path_emcs);
SUBJlist_EMCS = dir('EMC*.mat');

for i = 1:length(SUBJlist_EMCS)
    SUBJname_EMCS = SUBJlist_EMCS(i).name;
%     path1=([path SUBJname]);
%     cd(path1);
    data=load(SUBJname_EMCS);
    EMCS_aux(i,:,:) = data.aux;
end
t_emcs = data.time;
% figure
% plot(t_emc,EMCS_aux');


%%%%%% Import data for Group 2-b: LIS

cd(path_lis);
SUBJlist_LIS = dir('*.mat');

for i = 1:length(SUBJlist_LIS)
    SUBJname_LIS = SUBJlist_LIS(i).name;
%     path1=([path SUBJname]);
%     cd(path1);
    data=load(SUBJname_LIS);
    LIS_aux(i,:,:) = data.aux;
end
t_lis = data.time;
% figure
% plot(t_emc,EMCS_aux');




%%%%%% import data for group 3: MCS-

cd(path_mcs_m);
SUBJlist_MCS_m = dir('MCS_m_*.mat');

for i = 1:length(SUBJlist_MCS_m)
    SUBJname_MCS_m = SUBJlist_MCS_m(i).name;
%     path1=([path SUBJname]);
%     cd(path1);
    data=load(SUBJname_MCS_m);
    MCS_m_aux(i,:,:) = data.aux;

end
t_mcs_m = data.time;
% figure
% plot(t_mcs_m,MCS_m_aux');



%%%%%% import data for group 4: MCS+



cd(path_mcs_p);
SUBJlist_MCS_p = dir('MCS_p_*.mat');

for i = 1:length(SUBJlist_MCS_p)
    SUBJname_MCS_p = SUBJlist_MCS_p(i).name;
%     path1=([path SUBJname]);
%     cd(path1);
    data=load(SUBJname_MCS_p);
    MCS_p_aux(i,:,:) = data.aux;

end

t_mcs_p = data.time;
% figure
% plot(t_mcs_p,MCS_p_aux');

%%%%%% import data for group 4-b: MCS*



cd(path_mcs_ast);
SUBJlist_MCS_p = dir('MCS_ast_*.mat');

for i = 1:length(SUBJlist_MCS_p)
    SUBJname_MCS_p = SUBJlist_MCS_p(i).name;
%     path1=([path SUBJname]);
%     cd(path1);
    data=load(SUBJname_MCS_p);
    MCS_ast_aux(i,:,:) = data.aux;

end

t_mcs_ast = data.time;
% figure
% plot(t_mcs_ast,MCS_ast_aux');


%%%%%% import data for group 4-c: MCS+ and MCS-



cd(path_mcs);
SUBJlist_MCS = dir('MCS_*.mat');

for i = 1:length(SUBJlist_MCS)
    SUBJname_MCS = SUBJlist_MCS(i).name;
    data=load(SUBJname_MCS);
    MCS_aux(i,:,:) = data.aux;

end

t_mcs = data.time;
% figure
% plot(t_mcs,MCS_aux');


%%%%%% import data for group 5: UWS


cd(path_uws);
SUBJlist_UWS = dir('UWS_*.mat');

for i = 1:length(SUBJlist_UWS)
    SUBJname_UWS = SUBJlist_UWS(i).name;
%     path1=([path SUBJname]);
%     cd(path1);
    data=load(SUBJname_UWS);
    UWS_aux(i,:,:) = data.aux;

end
t_uws = data.time;
% figure
% plot(t_uws,UWS_aux');


%%%%%% import data for group 5-b: UWS*


cd(path_uws_ast);
SUBJlist_UWS_ast = dir('UWS_ast_*.mat');

for i = 1:length(SUBJlist_UWS_ast)
    SUBJname_UWS_ast = SUBJlist_UWS_ast(i).name;
%     path1=([path SUBJname]);
%     cd(path1);
    data=load(SUBJname_UWS_ast);
    UWS_ast_aux(i,:,:) = data.aux;

end
t_uws_ast = data.time;


%%%%%% import data for group 5-c: UWS-nonTBI

cd(path_uws_non_TBI);
SUBJlist_UWS = dir('UWS_*.mat');

for i = 1:length(SUBJlist_UWS)
    SUBJname_UWS = SUBJlist_UWS(i).name;
%     path1=([path SUBJname]);
%     cd(path1);
    data=load(SUBJname_UWS);
    UWS_noTBI_aux(i,:,:) = data.aux;

end
t_uws_no_tbi = data.time;

%%%%%% import data for group 5-d: UWS-TBI

cd(path_uws_TBI);
SUBJlist_UWS = dir('UWS_*.mat');

for i = 1:length(SUBJlist_UWS)
    SUBJname_UWS = SUBJlist_UWS(i).name;
%     path1=([path SUBJname]);
%     cd(path1);
    data=load(SUBJname_UWS);
    UWS_TBI_aux(i,:,:) = data.aux;

end
t_uws_tbi = data.time;


% figure
% plot(t_uws_ast,UWS_ast_aux');

%
% figure
% subplot(2,3,1); plot(t_control,Control_aux');
% subplot(2,3,2); plot(t_emc, EMCS_aux');
% subplot(2,3,3); plot(t_mcs_m, MCS_m_aux');
% subplot(2,3,4); plot(t_mcs_p, MCS_p_aux');
% subplot(2,3,5); plot(t_uws, UWS_aux');
% subplot(2,3,6); plot(t_uws_ast,UWS_ast_aux');


% Creating data for the tables 

% Control
mean_control = mean(mean(Control_aux))
std_control = std(mean(Control_aux))

% LIS
mean_LIS = mean(mean(LIS_aux))
std_LIS = std(mean(LIS_aux))

% EMCS
mean_EMCS = mean(mean(EMCS_aux))
std_EMCS = std(mean(EMCS_aux))

% MCS
mean_MCS = mean(mean(MCS_aux))
std_MCS = std(mean(MCS_aux))

% MCS+
mean_MCSp = mean(mean(MCS_p_aux))
std_MCSp = std(mean(MCS_p_aux))

% MCS-
mean_MCSm = mean(mean(MCS_m_aux))
std_MCSm = std(mean(MCS_m_aux))


% MCS*
mean_MCS_ast = mean(mean(MCS_ast_aux))
std_MCS_ast = std(mean(MCS_ast_aux))


% UWS
mean_UWS = mean(mean(UWS_aux))
std_UWS = std(mean(UWS_aux))


% UWS-nonTBI
mean_UWS_nonTBI = mean(mean(UWS_noTBI_aux))
std_UWS_nonTBI = std(mean(UWS_noTBI_aux))

% UWS-TBI
mean_UWS_TBI = mean(mean(UWS_TBI_aux))
std_UWS_TBI = std(mean(UWS_TBI_aux))


%%%  Statistics of Group Comparison:
cd(path_code);

[Cohens_d_control_EMCS, effect_size_r_control_EMCS] = effect_size(mean_control, mean_EMCS, std_control, std_EMCS)
[Cohens_d_control_MCS, effect_size_r_control_MCS] = effect_size(mean_control, mean_MCS, std_control, std_MCS)
[Cohens_d_control_MCS_p, effect_size_r_control_MCS_p] = effect_size(mean_control, mean_MCSp, std_control, std_MCSp)
[Cohens_d_control_MCS_m, effect_size_r_control_MCS_m] = effect_size(mean_control, mean_MCSm, std_control, std_MCSm)
[Cohens_d_control_MCS_ast, effect_size_r_control_MCS_ast] = effect_size(mean_control, mean_MCS_ast, std_control, std_MCS_ast)
[Cohens_d_control_UWS, effect_size_r_control_UWS] = effect_size(mean_control, mean_UWS, std_control, std_UWS)
[Cohens_d_control_UWS_nonTBI, effect_size_r_control_UWS_nonTBI] = effect_size(mean_control, mean_UWS_nonTBI, std_control, std_UWS_nonTBI)
[Cohens_d_control_UWS_TBI, effect_size_r_control_UWS_TBI] = effect_size(mean_control, mean_UWS_TBI, std_control, std_UWS_TBI)
[Cohens_d_control_LIS, effect_size_r_control_UWS_LIS] = effect_size(mean_control, mean_LIS, std_control, std_LIS)

%% Computing the area under the curve and the statistics for it
%
%
% AUC: Area Under the Curve or tpz
%
%
% 
%%%%%%%%%%%%



tpz_Control = trapz(Control_aux)/length(Control_aux);
tpz_EMCS = trapz(EMCS_aux)/length(EMCS_aux);
tpz_LIS = trapz(LIS_aux)/length(LIS_aux);
tpz_MCS = trapz(MCS_aux)/length(MCS_aux);
tpz_MCS_p = trapz(MCS_p_aux)/length(MCS_p_aux);
tpz_MCS_m = trapz(MCS_m_aux)/length(MCS_m_aux);
tpz_MCS_a = trapz(MCS_ast_aux)/length(MCS_ast_aux);
tpz_UWS = trapz(UWS_aux)/length(UWS_aux);
tpz_UWS_nonTBI = trapz(UWS_noTBI_aux)/length(UWS_noTBI_aux);
tpz_UWS_TBI = trapz(UWS_TBI_aux)/length(UWS_TBI_aux);


tpz_mean_Control = mean(tpz_Control);
tpz_mean_EMCS = mean(tpz_EMCS);
tpz_mean_LIS = mean(tpz_LIS);
tpz_mean_MCS = mean(tpz_MCS);
tpz_mean_MCS_p = mean(tpz_MCS_p);
tpz_mean_MCS_m = mean(tpz_MCS_m);
tpz_mean_MCS_a = mean(tpz_MCS_a);
tpz_mean_UWS =  mean(tpz_UWS);
tpz_mean_UWS_nonTBI = mean(tpz_UWS_nonTBI);
tpz_mean_UWS_TBI = mean(tpz_UWS_TBI);

tpz_STD_Control = std(tpz_Control);
tpz_STD_EMCS = std(tpz_EMCS);
tpz_STD_LIS = std(tpz_LIS);
tpz_STD_MCS = std(tpz_MCS);
tpz_STD_MCS_p = std(tpz_MCS_p);
tpz_STD_MCS_m = std(tpz_MCS_m);
tpz_STD_MCS_a = std(tpz_MCS_a);
tpz_STD_UWS =  std(tpz_UWS);
tpz_STD_UWS_nonTBI = std(tpz_UWS_nonTBI);
tpz_STD_UWS_TBI = std(tpz_UWS_TBI);

[h,p_conVSemcs]=ttest2(tpz_Control,tpz_EMCS, 0.05,'left');
[h,p_conVSlis]=ttest2(tpz_Control,tpz_LIS, 0.05,'left');
[h,p_conVSmcs]=ttest2(tpz_Control,tpz_MCS, 0.05,'left');
[h,p_conVSmcs_p]=ttest2(tpz_Control,tpz_MCS_p, 0.05,'left');
[h,p_conVSmcs_m]=ttest2(tpz_Control,tpz_MCS_m, 0.05,'left');
[h,p_conVSmcs_a]=ttest2(tpz_Control,tpz_MCS_a, 0.05,'right');
[h,p_conVSuws]=ttest2(tpz_Control,tpz_UWS, 0.05,'left');
[h,p_conVSuws_nonTBI]=ttest2(tpz_Control,tpz_UWS_nonTBI, 0.05,'right');
[h,p_conVSuws_TBI]=ttest2(tpz_Control,tpz_UWS_TBI, 0.05,'right');




%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%
%    Ploting 
%
%  
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


% EMCS
figure
y2_CC = mean(Control_aux);
z2_CC = std(Control_aux)/sqrt (length(Control_aux));
errorbar(t_control,y2_CC,z2_CC, 'b'); grid on;
hold on
y3_CC = mean (EMCS_aux);
%y3_CC(isnan(y3_CC)) = nanmedian(y3_CC);
z3_CC = std (EMCS_aux)/sqrt (length(EMCS_aux));
errorbar (t_emcs, y3_CC,z3_CC, 'r'); grid on; 
title( 'Control vs EMCS')
ylabel('Spectral Amplitude (SA)', 'FontSize',28,'FontWeight','bold','Color','k')
xlabel('time (min)');


% Statastical difference between Control and EMCS

[h_EMCS_aux,p_EMCS_aux] = ttest2(Control_aux,EMCS_aux,0.05)


% LIS
figure
y2_CC = mean(Control_aux);
z2_CC = std(Control_aux)/sqrt (length(Control_aux));
errorbar(t_control,y2_CC,z2_CC, 'b'); grid on;
hold on
y3_CC = mean (LIS_aux);
%y3_CC(isnan(y3_CC)) = nanmedian(y3_CC);
z3_CC = std (LIS_aux)/sqrt (length(LIS_aux));
errorbar (t_emcs, y3_CC,z3_CC, 'r'); grid on; 
title( 'Control vs LIS')
ylabel('Spectral Amplitude (SA)', 'FontSize',28,'FontWeight','bold','Color','k')
xlabel('time (min)');


% Statastical difference between Control and LIS

[h_LIS_aux,p_LIS_aux] = ttest2(Control_aux,LIS_aux,0.05)



% Statastical difference between  Control and MCS-

figure
y2_CC = mean(Control_aux);
z2_CC = std(Control_aux)/sqrt (length(Control_aux));
errorbar(t_control,y2_CC,z2_CC, 'b'); grid on;
hold on
y3_CC = mean (MCS_m_aux);
z3_CC = std (MCS_m_aux)/sqrt (length(MCS_m_aux));
errorbar (t_mcs_m, y3_CC,z3_CC, 'r'); grid on; 
title( 'Control vs MCS-')
ylabel('Spectral Amplitude (SA)', 'FontSize',28,'FontWeight','bold','Color','k')
xlabel('time (min)');


[h_MCS_m_aux,p_MCS_m_aux] = ttest2(Control_aux,MCS_m_aux,0.05)



% Statastical difference between t Control and MCS+


figure
y2_CC = mean(Control_aux);
z2_CC = std(Control_aux)/sqrt (length(Control_aux));
errorbar(t_control,y2_CC,z2_CC, 'b'); grid on;
hold on
y3_CC = mean (MCS_p_aux);
z3_CC = std (MCS_p_aux)/sqrt (length(MCS_p_aux));
errorbar (t_mcs_p, y3_CC,z3_CC, 'r'); grid on; 
title( 'Control vs MCS+')
ylabel('Spectral Amplitude (SA)', 'FontSize',28,'FontWeight','bold','Color','k')
xlabel('time (min)');




[h_MCS_p_aux,p_MCS_p_aux] = ttest2(Control_aux,MCS_p_aux,0.05)



% Statastical difference between t Control and MCS*


figure
y2_CC = mean(Control_aux);
z2_CC = std(Control_aux)/sqrt (length(Control_aux));
errorbar(t_control,y2_CC,z2_CC, 'b'); grid on;
hold on
y3_CC = mean (MCS_ast_aux);
z3_CC = std (MCS_ast_aux)/sqrt (length(MCS_ast_aux));
errorbar (t_mcs_ast, y3_CC,z3_CC, 'r'); grid on; 
title( 'Control vs MCS*')
ylabel('Spectral Amplitude (SA)', 'FontSize',28,'FontWeight','bold','Color','k')
xlabel('time (min)');


[h_MCS_ast_aux,p_MCS_ast_aux] = ttest2(Control_aux,MCS_ast_aux,0.05)


% Statastical difference between t Control and MCS


figure
y2_CC = mean(Control_aux);
z2_CC = std(Control_aux)/sqrt (length(Control_aux));
errorbar(t_control,y2_CC,z2_CC, 'b'); grid on;
hold on
y3_CC = mean (MCS_aux);
z3_CC = std (MCS_aux)/sqrt (length(MCS_aux));
errorbar (t_mcs, y3_CC,z3_CC, 'r'); grid on; 
title( 'Control vs MCS')
ylabel('Spectral Amplitude (SA)', 'FontSize',28,'FontWeight','bold','Color','k')
xlabel('time (min)');




[h_MCS_aux,p_MCS_aux] = ttest2(Control_aux,MCS_aux,0.05)


% Statistical difference between Control and UWS


figure
y2_CC = mean(Control_aux);
z2_CC = std(Control_aux)/sqrt (length(Control_aux));
errorbar(t_control,y2_CC,z2_CC, 'b'); grid on;
hold on
y3_CC = mean (UWS_aux);
z3_CC = std (UWS_aux)/sqrt (length(UWS_aux));
errorbar (t_uws, y3_CC,z3_CC, 'r'); grid on; 
title('Control vs UWS')
ylabel('Spectral Amplitude (SA)', 'FontSize',28,'FontWeight','bold','Color','k')
xlabel('time (min)');


[h_UWS_aux,p_UWS_aux] = ttest2(Control_aux,UWS_aux,0.05)


% % % Statistical difference between Control and UWS*
% % 
% % 
figure
y2_CC = mean(Control_aux);
z2_CC = std(Control_aux)/sqrt (length(Control_aux));
errorbar(t_control,y2_CC,z2_CC, 'b'); grid on;
hold on
%y3_CC = mean (UWS_ast_aux);
y3_CC = mean(UWS_ast_aux);
z3_CC = std (UWS_ast_aux)/sqrt (length(UWS_ast_aux));
errorbar(t_uws_ast, y3_CC,z3_CC, 'r'); grid on; 
title('Control vs UWS*')
ylabel('Spectral Amplitude (SA)', 'FontSize',28,'FontWeight','bold','Color','k')
xlabel('time (min)');


[h_UWS_ast_aux,p_UWS_ast_aux] = ttest2(Control_aux,UWS_ast_aux,0.05);

% Statistical difference between Control and UWS-nonTBI

figure
y2_CC = mean(Control_aux);
z2_CC = std(Control_aux)/sqrt (length(Control_aux));
errorbar(t_control,y2_CC,z2_CC, 'b'); grid on;
hold on
y3_CC = mean (UWS_noTBI_aux);
z3_CC = std (UWS_noTBI_aux)/sqrt (length(UWS_noTBI_aux));
errorbar (t_uws_no_tbi, y3_CC,z3_CC, 'r'); grid on; 
title('Control vs UWS-nonTBI')
ylabel('Spectral Amplitude (SA)', 'FontSize',28,'FontWeight','bold','Color','k')
xlabel('time (min)');


[h_UWS_nonTBI_aux,p_UWS_nonTBI_aux] = ttest2(Control_aux,UWS_noTBI_aux,0.05)


% Statistical difference between Control and UWS-TBI

figure
y2_CC = mean(Control_aux);
z2_CC = std(Control_aux)/sqrt (length(Control_aux));
errorbar(t_control,y2_CC,z2_CC, 'b'); grid on;
hold on
y3_CC = mean (UWS_TBI_aux);
z3_CC = std (UWS_TBI_aux)/sqrt (length(UWS_TBI_aux));
errorbar (t_uws_tbi, y3_CC,z3_CC, 'r'); grid on; 
title('Control vs UWS-TBI')
ylabel('Spectral Amplitude (SA)', 'FontSize',28,'FontWeight','bold','Color','k')
xlabel('time (min)');


[h_UWS_TBI_aux,p_UWS_TBI_aux] = ttest2(Control_aux,UWS_TBI_aux,0.05)

cd(path_code);

%% Plot of all the different results in one just figure
%  (ask by Steven Laureys)

y_control = mean(Control_aux);
y_EMCS =  mean(EMCS_aux);
y_LIS = mean(LIS_aux);
y_MCS_p = mean(MCS_p_aux);
y_MCS_m = mean(MCS_m_aux);
y_MCS_ast = mean(MCS_ast_aux);
y_MCS = mean(MCS_aux);
y_UWS = mean(UWS_aux);
y_UWS_nonTBI = mean(UWS_noTBI_aux);
y_UWS_TBI = mean(UWS_TBI_aux);

figure,
hh = plot(t_control, y_control, t_emcs, y_EMCS, t_lis, y_LIS, t_mcs, y_MCS, t_mcs_p, y_MCS_p, t_mcs_m, y_MCS_m, t_mcs_ast, y_MCS_ast, t_uws, y_UWS, t_uws_no_tbi, y_UWS_nonTBI,t_uws_tbi, y_UWS_TBI  );
legend(hh, 'Control', 'EMCS', 'LIS','MCS', 'MCS+ ', 'MCS- ', 'MCS*', 'UWS', 'UWS-nonTBI', 'UWS-TBI' )
title( 'Plot of Control, EMCS, LIS, MCS, MCS+, MCS-, MCS*, UWS, UWS-nonTBI, UWS-TBI')


%%% for Multiple Comparision

p_all_aux = [p_LIS_aux p_EMCS_aux p_MCS_aux p_MCS_m_aux p_MCS_p_aux p_MCS_p_aux p_UWS_aux p_UWS_TBI_aux p_UWS_nonTBI_aux];


[p_fdr, h_fdr] = fdr(p_all_aux, 0.09);
p_fdr
h_fdr

[p_mafdr] = mafdr(p_all_aux);
p_mafdr





% Statastical difference between two group for one tailed

%    [h_CC_1tailed,p_CC_1tailed] = ttest2(Control_aux,EMCS_aux,0.05,'left');
%h_CC_1tailed
%p_CC_1tailed


%for i = 1:65
%    [h_PL1(i),p_PL1(i)] = ttest2(sparsity_PL_normalised_Control(:,i),sparsity_PL_normalised_Patient(:,i),0.05,'left');
%end

%h_PL1
%p_PL1

%[p,h]=fdr(p_CC_Normalised,0.05);
%p


end