T1rho_maps3.m

%#######################################################################
%
%                  * T1rho Map Sensitivity 3 Program *
%
%          M-File which reads knee T1rho data with different spinlock
%     times in the cartilage regions from T1rho_maps_S501.mat which was
%     generated by T1rho_maps.m.  The difference in T1rho values
%     between using four or five spin lock times and the values from
%     using all seven spin lock times are plotted as histograms.  The
%     T1rho values are split between superficial and deep cartilage
%     layers.  Summary statistics on the T1rho differences are included
%     on the plots and written to a MS-Excel spreadsheet, 
%     T1rho_maps3_S501.xlsx.
%
%     NOTES:  1.  Must have MAT files T1rho_maps_S501.mat and
%             T1rho_S501.mat in the current directory.
%
%     03-Sep-2020 * Mack Gardner-Morse
%

%#######################################################################
%
% Load T1rho Values for Series 501 MRI Data
%
load T1rho_maps_S501.mat;
load T1rho_S501.mat fs slt;
%
% Initialize Arrays for Calculating the T1rho Differences
%
dT1rhonlss = cell(nrsl,1);
idv = cell(nrsl,1);
id1l = cell(nrsl,1);
id2l = cell(nrsl,1);
%
% Loop through Slices with ROIs to Calculate the T1rho Differences
%
for k = 1:nrsl          % Loop through slices with ROIs
%
   id1 = find(mask1(:,k));
   id2 = find(mask2(:,k));
   idc = find(maskc(:,k));
%
   id1l{k} = ismember(idc,id1);   % [~,id1l2] = intersect(idc,id1); - Logical index uses less space
   id2l{k} = ismember(idc,id2);
%
   idv{k} = T1rhonlss{k}(:,nt)>0&T1rhonlss{k}(:,nt)<100;   % Use values based on all seven (7) spin lock times
%
   dT1rhonlss{k} = T1rhonlss{k}-repmat(T1rhonlss{k}(:,nt),1,nt);
%
end
%
% Get Four and Five Spin Lock Times Combinations
%
idx = nszc(3)+1:nszc(5);     % Get 4 and 5 spin lock times combinations
nc = size(idx,2);
%
% Initialize Arrays for Looping Through the Spin Lock Times Combinations
%
binedg = -15:0.5:15;    % Bin edges for histograms
hnam = ['T1rho_maps3_hist_' fs '.ps']; % Histograms print file name
xnam = ['T1rho_maps3_' fs '.xlsx'];    % MS-Excel File
%
sltc = cell(nc,1);
%
n0 = zeros(nc,1);
mn0 = zeros(nc,1);
md0 = zeros(nc,1);
sd0 = zeros(nc,1);
%
n1 = zeros(nc,1);
mn1 = zeros(nc,1);
md1 = zeros(nc,1);
sd1 = zeros(nc,1);
%
n2 = zeros(nc,1);
mn2 = zeros(nc,1);
md2 = zeros(nc,1);
sd2 = zeros(nc,1);
%
% Loop through Combinations with Four or Five Spin Lock Times
%
for k = 1:nc            % Loop through combinations
%
   idxc = idx(k);       % Index to trial column
%
   [l,m] = ncombi(idx(k),nszc);
   sltc{k} = ncomb{l}(m,:);
   sltc{k} = int2str(slt(sltc{k})'); % Combination of spin lock times
   sltc{k} = regexprep(sltc{k},' +',', ');
   sltct = ['Spin lock times = ' sltc{k} ' ms']; % For plot titles
%
   hdat0 = [dT1rhonlss{1}(idv{1},idxc); ...
            dT1rhonlss{2}(idv{2},idxc); ...
            dT1rhonlss{3}(idv{3},idxc)];         % All three slices
%
   n0(k) = size(hdat0,1);
   mn0(k) =  mean(hdat0);
   md0(k) = median(hdat0);
   sd0(k) = std(hdat0);
%
% Plot Histograms of the Cartilage T1rho Differences
%
   hf = figure;
   orient tall;
%
   hdat1 = [dT1rhonlss{1}(idv{1}&id1l{1},idxc); ...
            dT1rhonlss{2}(idv{2}&id1l{2},idxc); ...
            dT1rhonlss{3}(idv{3}&id1l{3},idxc)]; % All three slices
%
   n1(k) = size(hdat1,1);
   mn1(k) =  mean(hdat1);
   md1(k) = median(hdat1);
   sd1(k) = std(hdat1);
%
   htxt1 = ['N = ' int2str(n1(k))];
   htxt2 = ['Mean \DeltaT1\rho = ' sprintf('%.2f',mn1(k))];
   htxt3 = ['Median \DeltaT1\rho = ' sprintf('%.2f',md1(k))];
   htxt4 = ['SD \DeltaT1\rho = ' sprintf('%.2f',sd1(k))];
   htxt = {htxt1; htxt2; htxt3; htxt4};
%
   h1 = subplot(2,1,1);
   histogram(hdat1,binedg,'FaceAlpha',1,'FaceColor',[0 0 0.8]);
   axlim = axis;
   text(75,axlim(4)/2,htxt,'FontSize',11,'FontWeight','bold');
   ylabel('Frequency','FontSize',12,'FontWeight','bold');
   title({[fs ' Trial ' int2str(idxc)]; sltct; ...
          'Superficial Layer'},'FontSize',16,'FontWeight','bold');
   axlim1 = axis;
   ht1 = text(-15,0.8*axlim1(4),htxt,'FontSize',11, ...
              'FontWeight','bold');
%
   hdat2 = [dT1rhonlss{1}(idv{1}&id2l{1},idxc); ...
            dT1rhonlss{2}(idv{2}&id2l{2},idxc); ...
            dT1rhonlss{3}(idv{3}&id2l{3},idxc)]; % All three slices
%
   n2(k) = size(hdat2,1);
   mn2(k) =  mean(hdat2);
   md2(k) =  median(hdat2);
   sd2(k) = std(hdat2);
%
   htxt1 = ['N = ' int2str(n2(k))];
   htxt2 = ['Mean \DeltaT1\rho = ' sprintf('%.2f',mn2(k))];
   htxt3 = ['Median \DeltaT1\rho = ' sprintf('%.2f',md2(k))];
   htxt4 = ['SD \DeltaT1\rho = ' sprintf('%.2f',sd2(k))];
   htxt = {htxt1; htxt2; htxt3; htxt4};
%
   h2 = subplot(2,1,2);
   histogram(hdat2,binedg,'FaceAlpha',1,'FaceColor',[0 0 0.8]);
   axlim = axis;
   text(75,axlim(4)/2,htxt,'FontSize',11,'FontWeight','bold');
   xlabel('T1rho Differences (ms)','FontSize',12, ...
          'FontWeight','bold');
   ylabel('Frequency','FontSize',12,'FontWeight','bold');
   title('Deep Layer','FontSize',16,'FontWeight','bold');
   axlim2 = axis;
   ht2 = text(-15,0.8*axlim2(4),htxt,'FontSize',11, ...
              'FontWeight','bold');
%
   if axlim2(4)<axlim1(4)
     set(h1,'YLimMode','manual');
     axis(h2,axlim1);
     ht2.Position(2) = 0.8*axlim1(4);
   else
     axis(h1,axlim2);
     set(h2,'YLimMode','manual');
     ht1.Position(2) = 0.8*axlim2(4);
   end
%
   if k==1
     print('-dpsc2','-r600','-fillpage',hnam);
   else
     print('-dpsc2','-r600','-fillpage','-append',hnam);
   end
%
end
%
% Find Best SD for Both Four and Five Spin Lock Times
%
[~,ids1] = sort(sd0(1:nsz(3)));
[~,ids2] = sort(sd0(nsz(3)+1:nc));
ids2 = ids2+nsz(3);
ids = [ids1; ids2];
%
% Get Variables in Sorted Order and Formatted for a Table
%
varnams = {'Trial #','Spin Lock Times','N SLTs','Layer','N','Mean', ...
           'Median','SD'};
%
idx = idx(ids);
idx = [idx; idx; idx];  % Trials
idx = idx(:);
%
sltc = sltc(ids);
sltc = [sltc'; sltc'; sltc'];
sltc = sltc(:);
%
nslts = [repmat(4,3*nsz(3),1); repmat(5,3*nsz(4),1)];
%
layer = repmat((1:3)',nc,1);
lays = {'Superficial';'Deep';'Combined'};
lays2 = lays(layer);
%
n = [n1(ids)'; n2(ids)'; n0(ids)'];
n = n(:);
%
mn = [mn1(ids)'; mn2(ids)'; mn0(ids)'];
mn = mn(:);
%
md = [md1(ids)'; md2(ids)'; md0(ids)'];
md = md(:);
%
sd = [sd1(ids)'; sd2(ids)'; sd0(ids)'];
sd = sd(:);
%
% Generate a Table and Write Data to a MS-Excel Spreadsheet
%
tabs = table(idx,sltc,nslts,lays2,n,mn,md,sd,'VariableNames',varnams);
writetable(tabs,xnam);
%
return