data/code/Stats/UWphoto_script_GLMmodeling.m

% Script to generate GLMs with the matched case info and volume statistics
% from both MRI and photo segmentations

%% load data

PHOTO_RECON_HOME='/home/acasamitjana/Results';%getenv('PHOTO_RECON_HOME');

figuresDir = fullfile(PHOTO_RECON_HOME,'figures');

% load(fullfile(figuresDir,'AdjustedCaseStats.mat'),'segVolumeInfo',...
%     'matchedInfo')

savedir = fullfile(figuresDir,'GLM');

if ~exist(savedir,'dir')
    mkdir(savedir)
end


%% sort out cases to remove
% removalLevel 1 - missing volumes and Hemmorhage removed
% removalLevel 2 - poorly segmented ventricles 
% removalLevel 3 - poor segmentations and defformation 
% removalLevel 4 - biasing ventricle volumes

removalLevel = 1;

removalFlag = (0<[segVolumeInfo.removaltype]) &...
    ([segVolumeInfo.removaltype] <=removalLevel);

segVolumeInfo_kept=segVolumeInfo(~removalFlag);

savepath = fullfile(savedir,['GLMresults_removalLevel_',...
    num2str(removalLevel)]);

%% get target demographics

flag_mrs = strcmp({segVolumeInfo_kept.segtype},'MRI');
flag_hrd = strcmp({segVolumeInfo_kept.segtype},'Hard');
flag_sft = strcmp({segVolumeInfo_kept.segtype},'Soft');


flag_female_disease = strcmp(matchedInfo.sex,'Female') & ...
    strcmp(matchedInfo.CognitiveStatus,'Dementia');

fd_demographics = matchedInfo(flag_female_disease,{'caseID','age'});

flag_male_disease = strcmp(matchedInfo.sex,'Male') & ...
    strcmp(matchedInfo.CognitiveStatus,'Dementia');

md_demographics = matchedInfo(flag_male_disease,{'caseID','age'});

flag_male_control = strcmp(matchedInfo.sex,'Male') & ...
    strcmp(matchedInfo.CognitiveStatus,'No dementia');

mc_demographics = matchedInfo(flag_male_control,{'caseID','age'});

%% make info structures
% these structures hold the label volumes, age and caseIDs for the selected
% cases that have not been excluded. They are split into separate
% structures for MRI, Hard reconstructions, Hard reconstructions with
% volume correction and Soft reconstruction.
%
% They are also split by cohort fd - female disease, md - male disease,
% mc - male control.

mri_strct_fd = struct();
mri_strct_fd(size(fd_demographics,1)) = struct();

mri_strct_md = struct();
mri_strct_md(size(md_demographics,1)) = struct();

mri_strct_mc = struct();
mri_strct_mc(size(mc_demographics,1)) = struct();


hrd_strct_fd = struct();
hrd_strct_fd(size(fd_demographics,1)) = struct();

hrd_strct_md = struct();
hrd_strct_md(size(md_demographics,1)) = struct();

hrd_strct_mc = struct();
hrd_strct_mc(size(mc_demographics,1)) = struct();


crct_strct_fd = struct();
crct_strct_fd(size(fd_demographics,1)) = struct();

crct_strct_md = struct();
crct_strct_md(size(md_demographics,1)) = struct();

crct_strct_mc = struct();
crct_strct_mc(size(mc_demographics,1)) = struct();


sft_strct_fd = struct();
sft_strct_fd(size(fd_demographics,1)) = struct();

sft_strct_md = struct();
sft_strct_md(size(md_demographics,1)) = struct();

sft_strct_mc = struct();
sft_strct_mc(size(mc_demographics,1)) = struct();


strfields = fieldnames(segVolumeInfo_kept);

%% get info fd

keep_flag = true(size(fd_demographics,1),1);

for il = 1:size(fd_demographics,1)
    
    selection_flag = strcmp({segVolumeInfo_kept.caseID},...
        fd_demographics.caseID(il));
    
    if any(selection_flag & flag_mrs)
        mri_strct_fd(il).age=fd_demographics.age(il);
        
        hrd_strct_fd(il).age=fd_demographics.age(il);
        
        crct_strct_fd(il).age=fd_demographics.age(il);
        
        sft_strct_fd(il).age=fd_demographics.age(il);
        
        for jl=1:length(strfields)
            mri_strct_fd(il).(strfields{jl})=segVolumeInfo_kept(...
                selection_flag & flag_mrs).(strfields{jl});
            
            hrd_strct_fd(il).(strfields{jl})=segVolumeInfo_kept(...
                selection_flag & flag_hrd).(strfields{jl});
            
            if jl<5
                crct_strct_fd(il).(strfields{jl})=segVolumeInfo_kept(...
                    selection_flag & flag_hrd).(strfields{jl});
            else
                crct_strct_fd(il).(strfields{jl})=segVolumeInfo_kept(...
                    selection_flag & flag_hrd).(strfields{jl})...
                    .*segVolumeInfo_kept(selection_flag &...
                    flag_hrd).volumeAdjustmentFactor;
            end
            
            sft_strct_fd(il).(strfields{jl})=segVolumeInfo_kept(...
                selection_flag & flag_sft).(strfields{jl});
        end
    else
        keep_flag(il)=false;
    end
    
    
    
end

mri_strct_fd=mri_strct_fd(keep_flag);

hrd_strct_fd=hrd_strct_fd(keep_flag);

crct_strct_fd=crct_strct_fd(keep_flag);

sft_strct_fd=sft_strct_fd(keep_flag);

%% get info md

keep_flag = true(size(md_demographics,1),1);

for il = 1:size(md_demographics,1)
    
    selection_flag = strcmp({segVolumeInfo_kept.caseID},...
        md_demographics.caseID(il));
    
    if any(selection_flag & flag_mrs)
        
        mri_strct_md(il).age=md_demographics.age(il);
        
        hrd_strct_md(il).age=md_demographics.age(il);
        
        sft_strct_md(il).age=md_demographics.age(il);
        
        for jl=1:length(strfields)
            mri_strct_md(il).(strfields{jl})=segVolumeInfo_kept(...
                selection_flag & flag_mrs).(strfields{jl});
            
            hrd_strct_md(il).(strfields{jl})=segVolumeInfo_kept(...
                selection_flag & flag_hrd).(strfields{jl});
            
            if jl<5
                crct_strct_md(il).(strfields{jl})=segVolumeInfo_kept(...
                    selection_flag & flag_hrd).(strfields{jl});
            else
                crct_strct_md(il).(strfields{jl})=segVolumeInfo_kept(...
                    selection_flag & flag_hrd).(strfields{jl})...
                    .*segVolumeInfo_kept(selection_flag &...
                    flag_hrd).volumeAdjustmentFactor;
            end
            
            sft_strct_md(il).(strfields{jl})=segVolumeInfo_kept(...
                selection_flag & flag_sft).(strfields{jl});
        end
    else
        keep_flag(il)=false;
    end
    
    
    
end

mri_strct_md=mri_strct_md(keep_flag);

hrd_strct_md=hrd_strct_md(keep_flag);

crct_strct_md=crct_strct_md(keep_flag);

sft_strct_md=sft_strct_md(keep_flag);

%% get info mc

keep_flag = true(size(mc_demographics,1),1);

for il = 1:size(mc_demographics,1)
    
    selection_flag = strcmp({segVolumeInfo_kept.caseID},...
        mc_demographics.caseID(il));
    
    if any(selection_flag & flag_mrs)
        
        mri_strct_mc(il).age=mc_demographics.age(il);
        
        hrd_strct_mc(il).age=mc_demographics.age(il);
        
        sft_strct_mc(il).age=mc_demographics.age(il);
        
        for jl=1:length(strfields)
            
            mri_strct_mc(il).(strfields{jl})=segVolumeInfo_kept(...
                selection_flag & flag_mrs).(strfields{jl});
            
            hrd_strct_mc(il).(strfields{jl})=segVolumeInfo_kept(...
                selection_flag & flag_hrd).(strfields{jl});
            
            if jl<5
                crct_strct_mc(il).(strfields{jl})=segVolumeInfo_kept(...
                    selection_flag & flag_hrd).(strfields{jl});
            else
                crct_strct_mc(il).(strfields{jl})=segVolumeInfo_kept(...
                    selection_flag & flag_hrd).(strfields{jl})...
                    .*segVolumeInfo_kept(selection_flag &...
                    flag_hrd).volumeAdjustmentFactor;
            end
            
            sft_strct_mc(il).(strfields{jl})=segVolumeInfo_kept(...
                selection_flag & flag_sft).(strfields{jl});
            
        end
    else
        keep_flag(il)=false;
    end
    
    
    
end

mri_strct_mc=mri_strct_mc(keep_flag);

hrd_strct_mc=hrd_strct_mc(keep_flag);

crct_strct_mc=crct_strct_mc(keep_flag);

sft_strct_mc=sft_strct_mc(keep_flag);


%% build GLM design matrix
% columns correspond to age, gender and disease respectively. For gender 1
% corresponds to female 0 to male. For disease 1 is dementia 0 is control.
% There is also a column of ones to account for the constant.

% numbers in each cohort
% N_fd - female diseased
N_fd = length(mri_strct_fd);
% N_md - male diseased
N_md = length(mri_strct_md);
% N_mc - male control
N_mc = length(mri_strct_mc);

N_total = N_fd+N_md+N_mc;

% predictors will be age, gender and disease, with a constant term
Design_mat = zeros(N_total,4);
Design_mat(:,4)=1;

% females with disease
for il= 1:N_fd
    
    Design_mat(il,1) = mri_strct_fd(il).age;
    Design_mat(il,2) = 1;
    Design_mat(il,3) = 1;
    
end

% males with disease
for il= 1:N_md
    
    Ientry = il+N_fd;
    
    Design_mat(Ientry,1) = mri_strct_md(il).age;
    Design_mat(Ientry,2) = 0;
    Design_mat(Ientry,3) = 1;
    
end

% males without disease
for il= 1:N_mc
    
    Ientry = il+N_fd+N_md;
    
    Design_mat(Ientry,1) = mri_strct_mc(il).age;
    Design_mat(Ientry,2) = 0;
    Design_mat(Ientry,3) = 0;
    
end

% remove column for gender due to lack of female controls
Design_mat_maleOnly=Design_mat(N_fd+1:end,[1,3,4]);


% Orthogonal designmat
Design_mat = gsog(Design_mat);


% Orthogonal designmat_male
Design_mat_maleOnly = gsog(Design_mat_maleOnly);


%% run model
% not going to use volume corrections at the moment because I'm not sure
% they are working well.

volume_fields = fieldnames(mri_strct_fd);

volume_flag = ~ismember(volume_fields,{'age','caseID','segtype',...
    'volumeAdjustmentFactor','removaltype','removalnotes'}');

volume_fields = volume_fields(volume_flag);


MRI_GLM_resultsStruct.N_femaleDisease = N_fd;
MRI_GLM_resultsStruct.N_maleDisease   = N_md;
MRI_GLM_resultsStruct.N_maleControl   = N_mc;
MRI_GLM_resultsStruct.N_total         = N_total;

Hrd_GLM_resultsStruct.N_femaleDisease = N_fd;
Hrd_GLM_resultsStruct.N_maleDisease   = N_md;
Hrd_GLM_resultsStruct.N_maleControl   = N_mc;
Hrd_GLM_resultsStruct.N_total         = N_total;

Crct_GLM_resultsStruct.N_femaleDisease = N_fd;
Crct_GLM_resultsStruct.N_maleDisease   = N_md;
Crct_GLM_resultsStruct.N_maleControl   = N_mc;
Crct_GLM_resultsStruct.N_total         = N_total;

Sft_GLM_resultsStruct.N_femaleDisease = N_fd;
Sft_GLM_resultsStruct.N_maleDisease   = N_md;
Sft_GLM_resultsStruct.N_maleControl   = N_mc;
Sft_GLM_resultsStruct.N_total         = N_total;


for il=1:length(volume_fields)
    
    %% MRI GLM
    
    Observations = [mri_strct_fd(:).(volume_fields{il}),...
        mri_strct_md(:).(volume_fields{il}),...
        mri_strct_mc(:).(volume_fields{il})]';
    
    [b,dev,stats] = glmfit(Design_mat,Observations,'normal','constant',...
        'off');
    
    MRI_GLM_resultsStruct.full.(volume_fields{il}).b = b;
    MRI_GLM_resultsStruct.full.(volume_fields{il}).dev = dev;
    MRI_GLM_resultsStruct.full.(volume_fields{il}).stats = stats;
    
    
    [b,dev,stats] = glmfit(Design_mat_maleOnly,Observations(N_fd+1:end),...
        'normal','constant','off');
    
    MRI_GLM_resultsStruct.male.(volume_fields{il}).b = b;
    MRI_GLM_resultsStruct.male.(volume_fields{il}).dev = dev;
    MRI_GLM_resultsStruct.male.(volume_fields{il}).stats = stats;
    
    
    %% Hard GLM
    
    Observations = [hrd_strct_fd(:).(volume_fields{il}),...
        hrd_strct_md(:).(volume_fields{il}),...
        hrd_strct_mc(:).(volume_fields{il})]';
    
    [b,dev,stats] = glmfit(Design_mat,Observations,'normal','constant',...
        'off');
    
    Hrd_GLM_resultsStruct.full.(volume_fields{il}).b = b;
    Hrd_GLM_resultsStruct.full.(volume_fields{il}).dev = dev;
    Hrd_GLM_resultsStruct.full.(volume_fields{il}).stats = stats;
    
    
    [b,dev,stats] = glmfit(Design_mat_maleOnly,Observations(N_fd+1:end),...
        'normal','constant','off');
    
    Hrd_GLM_resultsStruct.male.(volume_fields{il}).b = b;
    Hrd_GLM_resultsStruct.male.(volume_fields{il}).dev = dev;
    Hrd_GLM_resultsStruct.male.(volume_fields{il}).stats = stats;
    
    
    %% volume corrected Hard GLM
    
    Observations = [crct_strct_fd(:).(volume_fields{il}),...
        crct_strct_md(:).(volume_fields{il}),...
        crct_strct_mc(:).(volume_fields{il})]';
    
    [b,dev,stats] = glmfit(Design_mat,Observations,'normal','constant',...
        'off');
    
    Crct_GLM_resultsStruct.full.(volume_fields{il}).b = b;
    Crct_GLM_resultsStruct.full.(volume_fields{il}).dev = dev;
    Crct_GLM_resultsStruct.full.(volume_fields{il}).stats = stats;
    
    
    [b,dev,stats] = glmfit(Design_mat_maleOnly,Observations(N_fd+1:end),...
        'normal','constant','off');
    
    Crct_GLM_resultsStruct.male.(volume_fields{il}).b = b;
    Crct_GLM_resultsStruct.male.(volume_fields{il}).dev = dev;
    Crct_GLM_resultsStruct.male.(volume_fields{il}).stats = stats;
    
    
    %% Soft GLM
    
    Observations = [sft_strct_fd(:).(volume_fields{il}),...
        sft_strct_md(:).(volume_fields{il}),...
        sft_strct_mc(:).(volume_fields{il})]';
    
    [b,dev,stats] = glmfit(Design_mat,Observations,'normal','constant',...
        'off');
    
    Sft_GLM_resultsStruct.full.(volume_fields{il}).b = b;
    Sft_GLM_resultsStruct.full.(volume_fields{il}).dev = dev;
    Sft_GLM_resultsStruct.full.(volume_fields{il}).stats = stats;
    
    
    [b,dev,stats] = glmfit(Design_mat_maleOnly,Observations(N_fd+1:end),...
        'normal','constant','off');
    
    Sft_GLM_resultsStruct.male.(volume_fields{il}).b = b;
    Sft_GLM_resultsStruct.male.(volume_fields{il}).dev = dev;
    Sft_GLM_resultsStruct.male.(volume_fields{il}).stats = stats;
    
    
end

%% Save results

save(savepath,'segVolumeInfo_kept','*_strct_*','Design_mat*','*resultsStruct')