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UFA_quantificaton.m
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UFA_quantificaton.m
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function UFA_quantificaton(UFA_Folder,minlen,maxlen)
% AUTHOR : Gaoxing Zheng
% Institution: Zhongshan Hospital, Fudan University
% EMAIL CONTACT: zheng_gao_xing@163.com
% DATE: 2022-04-14
WM_tck_files = dir(fullfile(UFA_Folder,'/WMA_clustering_SWM/*.tck'));
U_fiber_name = {};
U_fiber_couts = [];
U_fiber_len = [];
for flag = 1:length(WM_tck_files)
fiber_name = WM_tck_files(flag).name;
fiber_name = fiber_name(1:length(fiber_name)-4);
if contains(fiber_name,'Sup')
unix(['tckstats ', [UFA_Folder,'/WMA_clustering_SWM/',fiber_name,'.tck'],' -dump ',[UFA_Folder,'/WMA_clustering_SWM/',fiber_name,'.txt'],' -force']);
fiber_txt = importdata([UFA_Folder,'/WMA_clustering_SWM/',fiber_name,'.txt']);
if ~isempty(fiber_txt)
U_fiber_name = [U_fiber_name; fiber_name];
U_fiber_couts = [U_fiber_couts, length(fiber_txt)];
U_fiber_len = [U_fiber_len, mean(fiber_txt)];
end
end
end
limit1 = ones(length(U_fiber_name),2); limit1(:,1) = 0; limit1(:,2) = ceil(max(U_fiber_couts)/10)*10;
prefer1 = ones(length(U_fiber_name),2); prefer1(:,1) = 10; prefer1(:,2) = 20;
prefer2 = ones(length(U_fiber_name),2); prefer2(:,1) = minlen+20; prefer2(:,2) = maxlen-20;
limit2 = ones(length(U_fiber_name),2); limit2(:,1) = minlen; limit2(:,2) = maxlen;
figure('Name','Number of fibers','NumberTitle','off'),UFA_draw_radar(U_fiber_couts,limit1,prefer1,U_fiber_name);
figure('Name','Mean fiber length','NumberTitle','off'),UFA_draw_radar(U_fiber_len,limit2,prefer2,U_fiber_name);
SWM_Path = [UFA_Folder,'/WMA_clustering_SWM'];
DWI_Path = [UFA_Folder,'/DWI/Tracking'];
if exist([SWM_Path,'/Stats_DTI_SWM'],'dir') == 0
mkdir([SWM_Path,'/Stats_DTI_SWM'])
end
SWM_FA = zeros(length(U_fiber_name),1);
SWM_MD = zeros(length(U_fiber_name),1);
SWM_AD = zeros(length(U_fiber_name),1);
SWM_RD = zeros(length(U_fiber_name),1);
for label = 1:length(U_fiber_name)
view_direction = U_fiber_name{label};
unix(['tcksample ',[SWM_Path,'/',view_direction,'.tck'],' ',[DWI_Path,'/dt_fa.mif'],' ',[SWM_Path,'/Stats_DTI_SWM/FA_',view_direction,'.txt'],' -stat_tck mean -force']);
unix(['tcksample ',[SWM_Path,'/',view_direction,'.tck'],' ',[DWI_Path,'/dt_md.mif'],' ',[SWM_Path,'/Stats_DTI_SWM/MD_',view_direction,'.txt'],' -stat_tck mean -force']);
unix(['tcksample ',[SWM_Path,'/',view_direction,'.tck'],' ',[DWI_Path,'/dt_ad.mif'],' ',[SWM_Path,'/Stats_DTI_SWM/AD_',view_direction,'.txt'],' -stat_tck mean -force']);
unix(['tcksample ',[SWM_Path,'/',view_direction,'.tck'],' ',[DWI_Path,'/dt_rd.mif'],' ',[SWM_Path,'/Stats_DTI_SWM/RD_',view_direction,'.txt'],' -stat_tck mean -force']);
% unix(['tcksample ',[SWM_Path,'/AnatomicalTracts/',view_direction,'.tck'],' ',[DWI_Path,'/dt_fa.mif'],' ',[SWM_Path,'/Stats_DTI_SWM/FA_',view_direction,'.txt'],' -stat_tck mean -force']);
%
% unix(['tcksample ',[SWM_Path,'/AnatomicalTracts/',view_direction,'.tck'],' ',[DWI_Path,'/dt_md.mif'],' ',[SWM_Path,'/Stats_DTI_SWM/MD_',view_direction,'.txt'],' -stat_tck mean -force']);
%
% unix(['tcksample ',[SWM_Path,'/AnatomicalTracts/',view_direction,'.tck'],' ',[DWI_Path,'/dt_ad.mif'],' ',[SWM_Path,'/Stats_DTI_SWM/AD_',view_direction,'.txt'],' -stat_tck mean -force']);
%
% unix(['tcksample ',[SWM_Path,'/AnatomicalTracts/',view_direction,'.tck'],' ',[DWI_Path,'/dt_rd.mif'],' ',[SWM_Path,'/Stats_DTI_SWM/RD_',view_direction,'.txt'],' -stat_tck mean -force']);
FA = importdata([SWM_Path,'/Stats_DTI_SWM/FA_',view_direction,'.txt']);
MD = importdata([SWM_Path,'/Stats_DTI_SWM/MD_',view_direction,'.txt']);
AD = importdata([SWM_Path,'/Stats_DTI_SWM/AD_',view_direction,'.txt']);
RD = importdata([SWM_Path,'/Stats_DTI_SWM/RD_',view_direction,'.txt']);
SWM_FA(label) = nanmean(FA.data);
SWM_MD(label) = nanmean(MD.data);
SWM_AD(label) = nanmean(AD.data);
SWM_RD(label) = nanmean(RD.data);
end
colors = colormap(hsv);
figure,ha = UFA_tightPlots(2, 2, 25, [1.3 1.3], [1.3 1.3], [1.3 1.3], [2 1.3], 'centimeters');
axes(ha(1)),
for i = 1:length(SWM_FA)
bar(i, SWM_FA(i),0.5,'facecolor',colors(i*12+10,:));hold on
end
set(gca,'XTickLabel',[])
hold off
ylabel('mean FA')
ylim([0.2 0.6])
axes(ha(2)),
for i = 1:length(SWM_MD)
bar(i,SWM_MD(i),0.5,'facecolor',colors(i*12 + 10,:));hold on
end
set(gca,'XTickLabel',[])
hold off
ylabel('mean MD')
ylim([4*10^(-4) 10*10^(-4)])
axes(ha(3)),
for i = 1:length(SWM_AD)
bar(i,SWM_AD(i),0.5,'facecolor',colors(i*12 + 10,:));hold on
end
xtextp = 1:length(SWM_AD);
ytextp = 0.59*10^(-3)*ones(1,length(xtextp));
text(xtextp, ytextp, U_fiber_name,'HorizontalAlignment','right','rotation',30,'Interpreter','none');
set(gca,'XTickLabel',[])
hold off
ylabel('mean AD')
ylim([0.6*10^(-3) 1.4*10^(-3)])
axes(ha(4)),
for i = 1:length(SWM_RD)
bar(i,SWM_RD(i),0.5,'facecolor',colors(i*12 + 10,:));hold on
end
xtextp = 1:length(SWM_RD);
ytextp = 2.9*10^(-4)*ones(1,length(xtextp));
text(xtextp, ytextp, U_fiber_name,'HorizontalAlignment','right','rotation',30,'Interpreter','none');
set(gca,'XTickLabel',[])
hold off
ylabel('mean RD')
ylim([3*10^(-4) 8*10^(-4)])