%% Find anomalies based on the segmentations


% Load the GM mask as well as the subject path list. In our case that would
% be the 2 files in the repository, but of course you need to construct
% yours first.

load('find_the_anomalies_github.mat')


parfor i = 1:11308
i

V1 = spm_vol(check_subject_list{i});
dummy_subj = spm_read_vols(V1);
dummy_subj = reshape(dummy_subj,1,[]);
dummy_subj = dummy_subj(GM_2_0_mask_0_1_threshold);    

Xmean(i,1) = mean(dummy_subj);
Xstd(i,1) = std(dummy_subj);

end


Xanom = [Xmean Xstd];
Xanom = (Xanom-mean(Xanom))./std(Xanom);


for i = 1:2

    anoms{i,1} = find(abs(Xanom(:,i))>3);
    anoms{i,2} = find(abs(Xanom(:,i))>4);
    anoms{i,3} = find(abs(Xanom(:,i))>5);
    anoms{i,4} = find(abs(Xanom(:,i))>6);
    
end


dummy3 = [];
dummy4 = [];
dummy5 = [];
dummy6 = [];

for i = 1:2
    
dummy3 = [dummy3; anoms{i,1}];
dummy4 = [dummy4; anoms{i,2}];
dummy5 = [dummy5; anoms{i,3}];
dummy6 = [dummy6; anoms{i,4}];

end


anoms_tab{1,1} = tabulate(dummy3);
anoms_tab{1,2} = tabulate(dummy4);
anoms_tab{1,3} = tabulate(dummy5);
anoms_tab{1,4} = tabulate(dummy6);


anoms_tab{1,1}(anoms_tab{1,1}(:,2)==0,:) = [];
anoms_tab{1,2}(anoms_tab{1,2}(:,2)==0,:) = [];
anoms_tab{1,3}(anoms_tab{1,3}(:,2)==0,:) = [];
anoms_tab{1,4}(anoms_tab{1,4}(:,2)==0,:) = [];


[~,ZZ] = sort(anoms_tab{1,1}(:,2));
anoms_tab_sorted{1,1} = flip(anoms_tab{1,1}(ZZ,:));

[~,ZZ] = sort(anoms_tab{1,2}(:,2));
anoms_tab_sorted{1,2} = flip(anoms_tab{1,2}(ZZ,:));

[~,ZZ] = sort(anoms_tab{1,3}(:,2));
anoms_tab_sorted{1,3} = flip(anoms_tab{1,3}(ZZ,:));

[~,ZZ] = sort(anoms_tab{1,4}(:,2));
anoms_tab_sorted{1,4} = flip(anoms_tab{1,4}(ZZ,:));


lala =     anoms_tab_sorted{1,2}(~ismember(anoms_tab_sorted{1,2}(:,1),anoms_tab_sorted{1,3}(:,1)),:);

for i = 1:length(lala)
    i
spm_image('display',check_subject_list{lala(i,1)})
pause
end

%%% FINALLY
anom_ids1 = find(abs(Xmean-mean(Xmean))./std(Xmean)>6);
anom_ids2 = find(abs(Xstd-mean(Xstd))./std(Xstd)>6);
anom_ids = unique([anom_ids1; anom_ids2]);

for i = 1:length(lala)
spm_image('display',check_subject_list{anom_ids(i)})
pause
end