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LoA_LoACM.m
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%% ----------------------------- LoA_MoACM --------------------------------
% Goal: Visualisation of the multi-observer (manual) gold fiducial marker
% localisation.
% The procedure is described in the paper:
% This method is provided withouht any warraty, and is presented for
% reproducibility purposes. The code cannot be used for medical purposed
% without any further check. No responsability can be related to the
% developers from any misuse of the code.
% Reproduction and modification of the code is possible upon reference to
% the original code and the published paper and as long as the new code is
% released under the same creative commons license.
% The code has been developed by Matteo Maspero in 2017 at UMC Utrecht.
% For info feel free to contact:
%% Housekeeping
clc; clear
close all;
%% Initialisation Params
% 1234 to save the filkse as pdf
Gen.savePng=1234;
% where to save the fig
filedir='./Figure';
% Pt to be visualised
Pt=1;
%% Parameters for Visualization
addpath('../utils/')
Size_ftn=20; Name_ftn='Times New Roman';
set(0,'DefaultAxesFontSize',Size_ftn,'DefaultAxesFontName',Name_ftn,'DefaultTextFontname','Times New Roman');
NumCol=12;
ColorObs=distinguishable_colors(5,{'w','k'});
ColorDist=distinguishable_colors(NumCol);
Marke={'o','x','+','.'};
MarkeSiz={20,20,20,60};
%% Data opening for multiple sequences
load('./Data/Pos_T1.mat')
Ptno=1:numel(CoGMRman1_ord);
%% Calculation LoA, LoACM & agreement Position
PosCent=zeros(3,3,17);
CM_CT=zeros(17,3);
CM_MRman1=CM_CT;CM_MRman2=CM_CT;CM_MRman3=CM_CT;CM_MRman4=CM_CT;CM_MRman5=CM_CT;
for ss=1:numel(Ptno)
CoGAll=zeros(3,3,5);
CM_CT(ss,:)=mean(CoGCT{ss});
CM_MRman1(ss,:)=mean(CoGMRman1_ord{ss}(1:size(CoGMRman1_ord{ss},1),:));
CM_MRman2(ss,:)=mean(CoGMRman2_ord{ss}(1:size(CoGMRman2_ord{ss},1),:));
CM_MRman3(ss,:)=mean(CoGMRman3_ord{ss}(1:size(CoGMRman3_ord{ss},1),:));
CM_MRman4(ss,:)=mean(CoGMRman4_ord{ss}(1:size(CoGMRman4_ord{ss},1),:));
CM_MRman5(ss,:)=mean(CoGMRman5_ord{ss}(1:size(CoGMRman5_ord{ss},1),:));
CM_Agre(ss,:)=mean([CM_MRman1(ss,:);CM_MRman2(ss,:);CM_MRman3(ss,:);...
CM_MRman4(ss,:);CM_MRman5(ss,:)]);
end
CMAll=cat(3,CM_MRman1,CM_MRman2,CM_MRman3,CM_MRman4,CM_MRman5);
Mat_CentTri=zeros(17,3,5);
for ssl=1:17
CoGAll=zeros(3,3);
CoGAll(1:size(CoGMRman1_ord{ss},1),:,1)=CoGMRman1_ord{ssl}(1:size(CoGMRman1_ord{ss},1),:);
CoGAll(1:size(CoGMRman2_ord{ss},1),:,2)=CoGMRman2_ord{ssl}(1:size(CoGMRman2_ord{ss},1),:);
CoGAll(1:size(CoGMRman3_ord{ss},1),:,3)=CoGMRman3_ord{ssl}(1:size(CoGMRman3_ord{ss},1),:);
CoGAll(1:size(CoGMRman4_ord{ss},1),:,4)=CoGMRman4_ord{ssl}(1:size(CoGMRman4_ord{ss},1),:);
CoGAll(1:size(CoGMRman5_ord{ss},1),:,5)=CoGMRman5_ord{ssl}(1:size(CoGMRman5_ord{ss},1),:);
% Loop to check consistency of the dimensions
jlls=0;
Complete=[0];
if size(CoGMRman1_ord{ss},1)==3
jlls=jlls+1;
Complete(jlls)=1;
end
if size(CoGMRman2_ord{ss},1)==3
jlls=jlls+1;
Complete(jlls)=2;
end
if size(CoGMRman3_ord{ss},1)==3
jlls=jlls+1;
Complete(jlls)=3;
end
if size(CoGMRman4_ord{ss},1)==3
jlls=jlls+1;
Complete(jlls)=4;
end
if size(CoGMRman5_ord{ss},1)==3
jlls=jlls+1;
Complete(jlls)=5;
end
PosCent(:,:,ssl)=mean(CoGAll(:,:,Complete),3 );
PosCentTri(:,:,ssl)=mean(sum(CoGAll(:,:,Complete),1)/3,3);
for ll=1:3
for ii=1:5
Mat_CentTri(ssl,ll,ii)=abs(CMAll(ssl,ll,ii)-CM_Agre(ssl,ll));
Dist1(ll,ii,ssl)=norm(CoGAll(ll,:,ii)-PosCent(ll,:,ssl));
Dist_CentTri(ssl,ll,ii)=norm(CMAll(ssl,ll,ii)-CM_Agre(ssl,ll));
Mat_CoGX(ssl,ll,ii)=abs(CoGAll(ll,1,ii)-PosCent(ll,1,ssl));
Mat_CoGY(ssl,ll,ii)=abs(CoGAll(ll,2,ii)-PosCent(ll,2,ssl));
Mat_CoGZ(ssl,ll,ii)=abs(CoGAll(ll,3,ii)-PosCent(ll,3,ssl));
end
rLoA(ll,ssl)=1.96*(std(Dist1(ll,:,ssl)));
rLoA_CM(ll,ssl)=1.96*(std(Mat_CentTri(ssl,ll,:)));
rLoA_X(ll,ssl)=1.96*(std(Mat_CoGX(ssl,ll,Complete)));
rLoA_Y(ll,ssl)=1.96*(std(Mat_CoGY(ssl,ll,Complete)));
rLoA_Z(ll,ssl)=1.96*(std(Mat_CoGZ(ssl,ll,Complete)));
end
end
%% Visualization Fiducials in 3D with triangle MR/CT & CT high Inter-observer
figure('Name','Representation Inter-observer on multiple sequences')
colormap(ColorDist)
view([-20 45]);
axis equal;hold on
plot3(CM_MRman1(Pt,1),CM_MRman1(Pt,2),CM_MRman1(Pt,3),'Color',ColorObs(1,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 1')
plot3(CM_MRman2(Pt,1),CM_MRman2(Pt,2),CM_MRman2(Pt,3),'Color',ColorObs(2,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 2')
plot3(CM_MRman3(Pt,1),CM_MRman3(Pt,2),CM_MRman3(Pt,3),'Color',ColorObs(3,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 3')
plot3(CM_MRman4(Pt,1),CM_MRman4(Pt,2),CM_MRman4(Pt,3),'Color',ColorObs(4,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 4')
plot3(CM_MRman5(Pt,1),CM_MRman5(Pt,2),CM_MRman5(Pt,3),'Color',ColorObs(5,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 5')
plot3(PosCentTri(1,1,Pt),PosCentTri(1,2,Pt),PosCentTri(1,3,Pt),'k',...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Agreement')
s=legend('show'); box(s,'off')
set(s,'Position',[ 0.3 0.78 0.0751 0.1273]);
for ll=1:3
if ll<=size(CoGMRman1_ord{Pt},1)
plot3(CoGMRman1_ord{Pt}(ll,1),CoGMRman1_ord{Pt}(ll,2),CoGMRman1_ord{Pt}(ll,3),'Color',ColorObs(1,:),...
'Marker',Marke{ll},'MarkerSize',MarkeSiz{ll},'LineWidth',1.5,'DisplayName','Obs 1')
end
if ll<=size(CoGMRman2_ord{Pt},1)
plot3(CoGMRman2_ord{Pt}(ll,1),CoGMRman2_ord{Pt}(ll,2),CoGMRman2_ord{Pt}(ll,3),'Color',ColorObs(2,:),...
'Marker',Marke{ll},'MarkerSize',MarkeSiz{ll},'LineWidth',1.5,'DisplayName','Obs 2')
end
if ll<=size(CoGMRman3_ord{Pt},1)
plot3(CoGMRman3_ord{Pt}(ll,1),CoGMRman3_ord{Pt}(ll,2),CoGMRman3_ord{Pt}(ll,3),'Color',ColorObs(3,:),...
'Marker',Marke{ll},'MarkerSize',MarkeSiz{ll},'LineWidth',1.5,'DisplayName','Obs 3')
end
if ll<=size(CoGMRman4_ord{Pt},1)
plot3(CoGMRman4_ord{Pt}(ll,1),CoGMRman4_ord{Pt}(ll,2),CoGMRman4_ord{Pt}(ll,3),'Color',ColorObs(4,:),...
'Marker',Marke{ll},'MarkerSize',MarkeSiz{ll},'LineWidth',1.5,'DisplayName','Obs 4')
end
if ll<=size(CoGMRman5_ord{Pt},1)
plot3(CoGMRman5_ord{Pt}(ll,1),CoGMRman5_ord{Pt}(ll,2),CoGMRman5_ord{Pt}(ll,3),'Color',ColorObs(5,:),...
'Marker',Marke{ll},'MarkerSize',MarkeSiz{ll},'LineWidth',1.5,'DisplayName','Obs 5')
end
plot3(PosCent(ll,1,Pt),PosCent(ll,2,Pt),PosCent(ll,3,Pt),'k',...
'Marker',Marke{ll},'MarkerSize',MarkeSiz{ll},'LineWidth',1.5,'DisplayName','Agreement')
end
xlabel('X [mm]');ylabel('Y [mm]');zlabel('Z [mm]'); % title(['Pt ',num2str(Pt)])
caxis([0,3])
% Center of Mass
annotation(gcf,'textbox',[0.11 0.765 0.137202377040826 0.14654282359762],...
... %s.Position + [0 s.Position(4) 0 0] ,...
'String',{'o FM 1','x FM 2','+ FM 3','\bullet Center Mass'},...
'FontSize',Size_ftn,'FontName',Name_ftn,'LineStyle','none',...
'FitBoxToText','on');
set(gcf,'Position',[1 1 1680 968])
grid on
if Gen.savePng==1234
printpdf(gcf,[filedir,'/InterObs_Pt',num2str(Pt,'%i'),'_Multiple.pdf'])
end
%% variable and Remove
rLoA_X_T1=rLoA_X;rLoA_Y_T1=rLoA_Y; rLoA_Z_T1=rLoA_Z;
rLoA_CM_T1=rLoA_CM;
clear CoG*
clear rLoA_X rLoA_CM rLoA_Y rLoA_Z
%% Open Single Sequence
load('./Data/Pos.mat')
%% Calculation LoA, LoACM & agreement Position
PosCent=zeros(3,3,17);
CM_CT=zeros(17,3);
CM_MRman1=CM_CT;CM_MRman2=CM_CT;CM_MRman3=CM_CT;CM_MRman4=CM_CT;CM_MRman5=CM_CT;
for ss=1:numel(Ptno)
CoGAll=zeros(3,3,5);
CM_CT(ss,:)=mean(CoGCT{ss});
CM_MRman1(ss,:)=mean(CoGMRman1_ord{ss}(1:size(CoGMRman1_ord{ss},1),:));
CM_MRman2(ss,:)=mean(CoGMRman2_ord{ss}(1:size(CoGMRman2_ord{ss},1),:));
CM_MRman3(ss,:)=mean(CoGMRman3_ord{ss}(1:size(CoGMRman3_ord{ss},1),:));
CM_MRman4(ss,:)=mean(CoGMRman4_ord{ss}(1:size(CoGMRman4_ord{ss},1),:));
CM_MRman5(ss,:)=mean(CoGMRman5_ord{ss}(1:size(CoGMRman5_ord{ss},1),:));
CM_Agre(ss,:)=mean([CM_MRman1(ss,:);CM_MRman2(ss,:);CM_MRman3(ss,:);...
CM_MRman4(ss,:);CM_MRman5(ss,:)]);
end
CMAll=cat(3,CM_MRman1,CM_MRman2,CM_MRman3,CM_MRman4,CM_MRman5);
Mat_CentTri=zeros(17,3,5);
for ssl=1:17
CoGAll=zeros(3,3);
CoGAll(1:size(CoGMRman1_ord{ss},1),:,1)=CoGMRman1_ord{ssl}(1:size(CoGMRman1_ord{ss},1),:);
CoGAll(1:size(CoGMRman2_ord{ss},1),:,2)=CoGMRman2_ord{ssl}(1:size(CoGMRman2_ord{ss},1),:);
CoGAll(1:size(CoGMRman3_ord{ss},1),:,3)=CoGMRman3_ord{ssl}(1:size(CoGMRman3_ord{ss},1),:);
CoGAll(1:size(CoGMRman4_ord{ss},1),:,4)=CoGMRman4_ord{ssl}(1:size(CoGMRman4_ord{ss},1),:);
CoGAll(1:size(CoGMRman5_ord{ss},1),:,5)=CoGMRman5_ord{ssl}(1:size(CoGMRman5_ord{ss},1),:);
jlls=0;
Complete=[0];
if size(CoGMRman1_ord{ss},1)==3
jlls=jlls+1;
Complete(jlls)=1;
end
if size(CoGMRman2_ord{ss},1)==3
jlls=jlls+1;
Complete(jlls)=2;
end
if size(CoGMRman3_ord{ss},1)==3
jlls=jlls+1;
Complete(jlls)=3;
end
if size(CoGMRman4_ord{ss},1)==3
jlls=jlls+1;
Complete(jlls)=4;
end
if size(CoGMRman5_ord{ss},1)==3
jlls=jlls+1;
Complete(jlls)=5;
end
PosCent(:,:,ssl)=mean(CoGAll(:,:,Complete),3 );
PosCentTri(:,:,ssl)=mean(sum(CoGAll(:,:,Complete),1)/3,3);
for ll=1:3
for ii=1:5
Mat_CentTri(ssl,ll,ii)=abs(CMAll(ssl,ll,ii)-CM_Agre(ssl,ll));
Dist1(ll,ii,ssl)=norm(CoGAll(ll,:,ii)-PosCent(ll,:,ssl));
Dist_CentTri(ssl,ll,ii)=norm(CMAll(ssl,ll,ii)-CM_Agre(ssl,ll));
Mat_CoGX(ssl,ll,ii)=abs(CoGAll(ll,1,ii)-PosCent(ll,1,ssl));
Mat_CoGY(ssl,ll,ii)=abs(CoGAll(ll,2,ii)-PosCent(ll,2,ssl));
Mat_CoGZ(ssl,ll,ii)=abs(CoGAll(ll,3,ii)-PosCent(ll,3,ssl));
end
rLoA(ll,ssl)=1.96*(std(Dist1(ll,:,ssl)));
rLoA_CM(ll,ssl)=1.96*(std(Mat_CentTri(ssl,ll,:)));
rLoA_X(ll,ssl)=1.96*(std(Mat_CoGX(ssl,ll,Complete)));
rLoA_Y(ll,ssl)=1.96*(std(Mat_CoGY(ssl,ll,Complete)));
rLoA_Z(ll,ssl)=1.96*(std(Mat_CoGZ(ssl,ll,Complete)));
end
end
%% Visualization Fiducials in 3D with triangle MR/CT & CT high Inter-observer
figure('Name','Representation Inter-observer on single sequence')
colormap(ColorDist)
view([-20 45]);
axis equal;hold on
plot3(CM_MRman1(Pt,1),CM_MRman1(Pt,2),CM_MRman1(Pt,3),'Color',ColorObs(1,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 1')
plot3(CM_MRman2(Pt,1),CM_MRman2(Pt,2),CM_MRman2(Pt,3),'Color',ColorObs(2,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 2')
plot3(CM_MRman3(Pt,1),CM_MRman3(Pt,2),CM_MRman3(Pt,3),'Color',ColorObs(3,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 3')
plot3(CM_MRman4(Pt,1),CM_MRman4(Pt,2),CM_MRman4(Pt,3),'Color',ColorObs(4,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 4')
plot3(CM_MRman5(Pt,1),CM_MRman5(Pt,2),CM_MRman5(Pt,3),'Color',ColorObs(5,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 5')
plot3(PosCentTri(1,1,Pt),PosCentTri(1,2,Pt),PosCentTri(1,3,Pt),'k',...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Agreement')
s=legend('show'); box(s,'off')
set(s,'Position',[ 0.3 0.78 0.0751 0.1273]);
for ll=1:3
view([-20 45]);
axis equal;hold on
% after order
if ll<=size(CoGMRman1_ord{Pt},1)
plot3(CoGMRman1_ord{Pt}(ll,1),CoGMRman1_ord{Pt}(ll,2),CoGMRman1_ord{Pt}(ll,3),'Color',ColorObs(1,:),...
'Marker',Marke{ll},'MarkerSize',MarkeSiz{ll},'LineWidth',1.5,'DisplayName','Obs 1')
end
if ll<=size(CoGMRman2_ord{Pt},1)
plot3(CoGMRman2_ord{Pt}(ll,1),CoGMRman2_ord{Pt}(ll,2),CoGMRman2_ord{Pt}(ll,3),'Color',ColorObs(2,:),...
'Marker',Marke{ll},'MarkerSize',MarkeSiz{ll},'LineWidth',1.5,'DisplayName','Obs 2')
end
if ll<=size(CoGMRman3_ord{Pt},1)
plot3(CoGMRman3_ord{Pt}(ll,1),CoGMRman3_ord{Pt}(ll,2),CoGMRman3_ord{Pt}(ll,3),'Color',ColorObs(3,:),...
'Marker',Marke{ll},'MarkerSize',MarkeSiz{ll},'LineWidth',1.5,'DisplayName','Obs 3')
end
if ll<=size(CoGMRman4_ord{Pt},1)
plot3(CoGMRman4_ord{Pt}(ll,1),CoGMRman4_ord{Pt}(ll,2),CoGMRman4_ord{Pt}(ll,3),'Color',ColorObs(4,:),...
'Marker',Marke{ll},'MarkerSize',MarkeSiz{ll},'LineWidth',1.5,'DisplayName','Obs 4')
end
if ll<=size(CoGMRman5_ord{Pt},1)
plot3(CoGMRman5_ord{Pt}(ll,1),CoGMRman5_ord{Pt}(ll,2),CoGMRman5_ord{Pt}(ll,3),'Color',ColorObs(5,:),...
'Marker',Marke{ll},'MarkerSize',MarkeSiz{ll},'LineWidth',1.5,'DisplayName','Obs 5')
end
plot3(PosCent(ll,1,Pt),PosCent(ll,2,Pt),PosCent(ll,3,Pt),'k',...
'Marker',Marke{ll},'MarkerSize',MarkeSiz{ll},'LineWidth',1.5,'DisplayName','Agreement')
end
xlabel('X [mm]');ylabel('Y [mm]');zlabel('Z [mm]'); % title(['Pt ',num2str(Pt)])
caxis([0,3])
% Center of Mass
annotation(gcf,'textbox',[0.11 0.765 0.137202377040826 0.14654282359762],...
... %s.Position + [0 s.Position(4) 0 0] ,...
'String',{'o FM 1','x FM 2','+ FM 3','\bullet Center Mass'},...
'FontSize',Size_ftn,'FontName',Name_ftn,'LineStyle','none',...
'FitBoxToText','on');
plot3(CM_MRman1(Pt,1),CM_MRman1(Pt,2),CM_MRman1(Pt,3),'Color',ColorObs(1,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 1')
plot3(CM_MRman2(Pt,1),CM_MRman2(Pt,2),CM_MRman2(Pt,3),'Color',ColorObs(2,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 2')
plot3(CM_MRman3(Pt,1),CM_MRman3(Pt,2),CM_MRman3(Pt,3),'Color',ColorObs(3,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 3')
plot3(CM_MRman4(Pt,1),CM_MRman4(Pt,2),CM_MRman4(Pt,3),'Color',ColorObs(4,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 4')
plot3(CM_MRman5(Pt,1),CM_MRman5(Pt,2),CM_MRman5(Pt,3),'Color',ColorObs(5,:),...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Obs 5')
plot3(PosCentTri(1,1,Pt),PosCentTri(1,2,Pt),PosCentTri(1,3,Pt),'k',...
'Marker',Marke{ll+1},'MarkerSize',MarkeSiz{ll+1},'LineWidth',1.5,'DisplayName','Agreement')
set(gcf,'Position',[1 1 1680 968])
grid on
if Gen.savePng==1234
printpdf(gcf,[filedir,'/InterObs_Pt',num2str(Pt,'%i'),'_Single.pdf'])
end
%% Single FM
th=2;
figure;set(gcf,'Position',[1 1 1680 960])
Col=distinguishable_colors(3);
subplot(321);
b=bar(rLoA_X');line([0.5 17.5],[th th],'Color','k','LineStyle','-.','LineWidth',1.5)
title('Single sequence');
line([0.5 17.5],[th-1 th-1],'Color','k','LineStyle','--','LineWidth',1.5)
%legend({'FM 1' 'FM 2' 'FM 3','2 mm','1mm'},'Location','Best')%,'Position',[0.6818 0.8047 0.1486 0.1587]);
for ii=1:3; b(ii).FaceColor=Col(ii,:); end
ylim([-0.5 10.5])
%legend('boxoff'); %title('Limit of Agreement');
ylabel('LoA_X [mm]','FontSize',Size_ftn,'FontName',Name_ftn)
xlim([0.5 17.5]);
set(gca,'Position',[0.05 0.67 0.455 0.28],'XTickLabel',{'','','','','','','',''})
subplot(322);
b=bar(rLoA_X_T1');line([0.5 17.5],[th th],'Color','k','LineStyle','-.','LineWidth',1.5)
title('Multiple sequences');
line([0.5 17.5],[th-1 th-1],'Color','k','LineStyle','--','LineWidth',1.5)
legend({'FM 1' 'FM 2' 'FM 3','2 mm','1mm'},'Location','Best')%,'Position',[0.6818 0.8047 0.1486 0.1587]);
for ii=1:3; b(ii).FaceColor=Col(ii,:); end
ylim([-0.5 10.5])
legend('boxoff'); %title('Limit of Agreement');
xlim([0.5 17.5]);
set(gca,'Position',[0.535 0.67 0.455 0.28],'XTickLabel',{'','','','','','','',''})
subplot(323); b=bar(rLoA_Y');ylabel('LoA_Y [mm]','FontSize',Size_ftn,'FontName',Name_ftn)
for ii=1:3; b(ii).FaceColor=Col(ii,:); end
ylim([-0.5 10.5])
xlim([0.5 17.5]); line([0.5 17.5],[th th],'Color','k','LineStyle','-.','LineWidth',1.5)
line([0.5 17.5],[th-1 th-1],'Color','k','LineStyle','--','LineWidth',1.5)
set(gca,'Position',[0.05 0.375 0.455 0.28],'XTickLabel',{'','','','','','','',''})
subplot(324); b=bar(rLoA_Y_T1');
for ii=1:3; b(ii).FaceColor=Col(ii,:); end
ylim([-0.5 10.5])
xlim([0.5 17.5]); line([0.5 17.5],[th th],'Color','k','LineStyle','-.','LineWidth',1.5)
line([0.5 17.5],[th-1 th-1],'Color','k','LineStyle','--','LineWidth',1.5)
set(gca,'Position',[0.535 0.375 0.455 0.28],'XTickLabel',{'','','','','','','',''})
subplot(325); b=bar(rLoA_Z'); ylabel('LoA_Z [mm]','FontSize',Size_ftn,'FontName',Name_ftn)
for ii=1:3; b(ii).FaceColor=Col(ii,:); end
ylim([-0.5 10.5])
xlim([0.5 17.5]); line([0.5 17.5],[th th],'Color','k','LineStyle','-.','LineWidth',1.5)
line([0.5 17.5],[th-1 th-1],'Color','k','LineStyle','--','LineWidth',1.5)
xlabel('Patient','FontSize',Size_ftn,'FontName',Name_ftn)
set(gca,'Position',[0.05 0.08 0.455 0.28])
subplot(326); b=bar(rLoA_Z_T1');
for ii=1:3; b(ii).FaceColor=Col(ii,:); end
ylim([-0.5 10.5])
xlim([0.5 17.5]); line([0.5 17.5],[th th],'Color','k','LineStyle','-.','LineWidth',1.5)
line([0.5 17.5],[th-1 th-1],'Color','k','LineStyle','--','LineWidth',1.5)
xlabel('Patient','FontSize',Size_ftn,'FontName',Name_ftn)
set(gca,'Position',[0.535 0.08 0.455 0.28])
if Gen.savePng==1234
%saveas(gcf,[filedir,'/LoA_perFM_AllPt'],'png')
%saveas(gcf,[filedir,'/LoA_perFM_AllPt.fig'])
printpdf(gcf,[filedir,'/LoA_perFM_AllPt.pdf'])
% saveas(gcf,[filedir,'/LoA_perFM_AllPt.eps'],'epsc')
% saveas(gcf,[filedir,'/LoA_perFM_AllPt.tif'])
end
%% CM
th=1;
figure;
set(gcf,'Position',[1 1 1640 500])
subplot(121)
b=bar(rLoA_CM');
title('Single sequence');
ylabel('LoA_{CM} [mm]'); xlabel('Patient')
xlim([0.5 17.5]);
line([0.5 17.5],[th+1 th+1],'Color','k','LineStyle','-.','LineWidth',1.5)
line([0.5 17.5],[th th],'Color','k','LineStyle','--','LineWidth',1.5)
%,'Position',[0.6818 0.8047 0.1486 0.1587]);
for ii=1:3; b(ii).FaceColor=Col(ii,:); end
ylim([-0.15 6])
%legend({'X' 'Y' 'Z','2 mm','1mm'},'Location','Best');
%legend('boxoff'); %title('Limit of Agreement');
ylabel('LoA_{CM} [mm]','FontSize',Size_ftn,'FontName',Name_ftn)
xlim([0.5 17.5]);
set(gca,'Position',[0.05 0.145 0.455 0.78])
subplot(122)
b=bar(rLoA_CM_T1');
title('Multiple sequences');
%ylabel('LoA_{CM} [mm]');
xlabel('Patient')
xlim([0.5 17.5]);
line([0.5 17.5],[th+1 th+1],'Color','k','LineStyle','-.','LineWidth',1.5)
line([0.5 17.5],[th th],'Color','k','LineStyle','--','LineWidth',1.5)
%,'Position',[0.6818 0.8047 0.1486 0.1587]);
for ii=1:3; b(ii).FaceColor=Col(ii,:); end
ylim([-0.15 6])
legend({'X' 'Y' 'Z','2 mm','1mm'},'Location','Best');
legend('boxoff'); %title('Limit of Agreement');
set(gca,'Position',[0.535 0.145 0.455 0.78])
%ylabel('X [mm]','FontSize',Size_ftn,'FontName',Name_ftn)
xlim([0.5 17.5]);
[a,b,c]=ttest(rLoA_CM_T1(:)',rLoA_CM(:)');
if Gen.savePng==1234
%saveas(gcf,[filedir,'/LoA_CM_AllPt'],'png')
%saveas(gcf,[filedir,'/LoA_CM_AllPt.fig'])
printpdf(gcf,[filedir,'/LoA_CM_AllPt.pdf'])
% saveas(gcf,[filedir,'/LoA_CM_AllPt.eps'],'epsc')
% saveas(gcf,[filedir,'/LoA_CM_AllPt.tif'])
end