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GannetFitAM.m
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GannetFitAM.m
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function [MRS_struct] = GannetFitAM(MRS_struct)
%
% MRS_struct = structure with data loaded from MRSLoadPfiles
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Gannet 2.0 version of Gannet Fit - analysis tool for GABA-edited MRS.
% Need some new sections like
% 1. GABA Fit
% 2. Water Fit
% 3. Cr Fit
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
FIT_LSQCURV = 0;
FIT_NLINFIT = 1;
fit_method = FIT_NLINFIT; %FIT_NLINFIT;
waterfit_method = FIT_NLINFIT;
GABAData=MRS_struct.spec.diff;
freq=MRS_struct.spec.freq;
if strcmp(MRS_struct.p.Reference_compound,'H2O')
WaterData=MRS_struct.spec.water;
end
MRS_struct.versionfit = '140709';
disp(['GABA Fit Version is ' MRS_struct.versionfit ]);
fitwater=1;
numscans=size(GABAData);
numscans=numscans(1);
%110624
epsdirname = [ './MRSfit_' datestr(clock,'yymmdd') ];
for ii=1:numscans
MRS_struct.gabafile{ii};
if strcmp(MRS_struct.p.target,'GABA')
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 1. GABA Fit
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% ...from GaussModel;
% x(1) = gaussian amplitude
% x(2) = 1/(2*sigma^2)
% x(3) = centre freq of peak
% x(4) = amplitude of linear baseline
% x(5) = constant amplitude offset
%Hard code it to fit from 2.79 ppm to 3.55 ppm
z=abs(MRS_struct.spec.freq-3.55);
lowerbound=find(min(z)==z);
z=abs(MRS_struct.spec.freq-2.79);%2.75
upperbound=find(min(z)==z);
freqbounds=lowerbound:upperbound;
plotbounds=(lowerbound-150):(upperbound+150);
maxinGABA=max(real(GABAData(MRS_struct.ii,freqbounds)));
% smarter estimation of baseline params, Krish's idea (taken from Johns
% code; NAP 121211
grad_points = (real(GABAData(ii,upperbound)) - real(GABAData(ii,lowerbound))) ./ ...
(upperbound - lowerbound); %in points
LinearInit = grad_points ./ (MRS_struct.spec.freq(1) - MRS_struct.spec.freq(2)); %in ppm
constInit = (real(GABAData(ii,upperbound)) + real(GABAData(ii,lowerbound))) ./2;
xval = [ 1:(upperbound-lowerbound+1) ];
linearmodel = grad_points .* xval + GABAData(ii,lowerbound);
%End copy code
resnorm=zeros([numscans size(freqbounds,2)]);
GaussModelInit = [maxinGABA -90 3.026 -LinearInit constInit]; %default in 131016
lb = [0 -200 2.87 -40*maxinGABA -2000*maxinGABA]; %NP; our bounds are 0.03 less due to creatine shift
ub = [4000*maxinGABA -40 3.12 40*maxinGABA 1000*maxinGABA];
options = optimset('lsqcurvefit');
options = optimset(options,'Display','off','TolFun',1e-10,'Tolx',1e-10,'MaxIter',1e5);
nlinopts = statset('nlinfit');
nlinopts = statset(nlinopts, 'MaxIter', 1e5);
%Fitting to a Gaussian model happens here
[GaussModelParam(ii,:),resnorm,residg] = lsqcurvefit(@(xdummy,ydummy) GaussModel_area(xdummy,ydummy), ...
GaussModelInit, freq(freqbounds),real(GABAData(ii,freqbounds)), ...
lb,ub,options);
residg = -residg;
if(fit_method == FIT_NLINFIT)
GaussModelInit = GaussModelParam(ii,:);
% 1111013 restart the optimisation, to ensure convergence
for fit_iter = 1:100
[GaussModelParam(ii,:), residg, J, COVB, MSE] = nlinfit(freq(freqbounds), real(GABAData(ii,freqbounds)), ... % J, COBV, MSE edited in
@(xdummy,ydummy) GaussModel_area(xdummy,ydummy), ...
GaussModelInit, ...
nlinopts);
MRS_struct.out.fitparams_iter(fit_iter,:,ii) = GaussModelParam(ii,:);
GaussModelInit = GaussModelParam(ii,:);
ci = nlparci(GaussModelParam(ii,:), residg,'covar',COVB); %copied over
end
end
GABAheight = GaussModelParam(ii,1);
% FitSTD reports the standard deviation of the residuals / gaba HEIGHT
MRS_struct.out.GABAFitError(ii) = 100*std(residg)/GABAheight;
% This sets GabaArea as the area under the curve.
MRS_struct.out.GABAArea(ii)=GaussModelParam(ii,1)./sqrt(-GaussModelParam(ii,2))*sqrt(pi);
sigma = ( 1 / (2 * (abs(GaussModelParam(ii,2)))) ).^(1/2);
MRS_struct.out.GABAFWHM(ii) = abs( (2* MRS_struct.p.LarmorFreq) * sigma);
MRS_struct.out.GABAModelFit(ii,:)=GaussModelParam(ii,:);
elseif strcmp(MRS_struct.p.target,'GSH')
%GSH fit
%Hard code it to fit from 2 ppm to 4 ppm
z=abs(MRS_struct.spec.freq-4);
lowerbound=find(min(z)==z);
z=abs(MRS_struct.spec.freq-2);
upperbound=find(min(z)==z);
freqbounds=lowerbound:upperbound;
plotbounds=(lowerbound-150):(upperbound+150);
offset = (mean(MRS_struct.spec.diff(ii, freqbounds(1:10)),2) + mean(MRS_struct.spec.diff(ii, freqbounds((end-9):end)),2))/2;
slope = (mean(MRS_struct.spec.diff(ii, freqbounds(1:10)),2) - mean(MRS_struct.spec.diff(ii, freqbounds((end-9):end)),2))/(MRS_struct.spec.freq(freqbounds(1)) - MRS_struct.spec.freq(freqbounds(end)));
peak_amp = 0.03; %Presumably this won't work for some data... for now it seems to work.
initx = [peak_amp*0.4 -200 2.97 peak_amp*0.8 -500 2.75 peak_amp -300 2.61 peak_amp*0.6 -600 2.46 peak_amp*0.5 -600 2.39 offset slope 0];
lb = [0 -5000 2.8 0 -5000 2.68 0 -5000 2.53 0 -5000 2.43 0 -5000 2.3 -1 -1 -1];
ub = [1 0 3.2 1 0 2.8 1 0 2.68 1 0 2.53 1 0 2.43 1 1 1];
options = optimset('lsqcurvefit');
options = optimset(options,'Display','off','TolFun',1e-10,'Tolx',1e-10,'MaxIter',1e5);
nlinopts = statset('nlinfit');
nlinopts = statset(nlinopts, 'MaxIter', 1e5);
[FiveGaussModelParam(ii,:),resnorm,residg] = lsqcurvefit(@(xdummy,ydummy) FiveGaussModel(xdummy,ydummy), ...
initx, MRS_struct.spec.freq(freqbounds),real(MRS_struct.spec.diff(ii,freqbounds)), ...
lb,ub,options);
residg = -residg;
GSHGaussModelParam(ii,:)=FiveGaussModelParam(ii,:);
GSHGaussModelParam(ii,4:3:13)=0;
NAAGaussModelParam(ii,:)=FiveGaussModelParam(ii,:);
NAAGaussModelParam(1)=0;
BaselineModelParam=GSHGaussModelParam;
BaselineModelParam(ii,1)=0;
MRS_struct.out.GABAArea(ii)=real(sum(FiveGaussModel(GSHGaussModelParam(ii,:), MRS_struct.spec.freq(freqbounds))-FiveGaussModel(BaselineModelParam(ii,:), MRS_struct.spec.freq(freqbounds))))*(MRS_struct.spec.freq(1)-MRS_struct.spec.freq(2));
%Not sure how to handle fit error. For now, do whole range
GABAheight = GSHGaussModelParam(ii,1);
MRS_struct.out.GABAFitError(ii)= 100*std(residg)/GABAheight;
else
error('Fitting MRS_struct.p.target not recognised');
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 1A. Start up the output figure
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
fignum = 102;
if(ishandle(fignum))
close(fignum)
end
h=figure(fignum);
set(h, 'Position', [100, 100, 1000, 707]);
set(h,'Color',[1 1 1]);
figTitle = ['GannetFit Output'];
set(gcf,'Name',figTitle,'Tag',figTitle, 'NumberTitle','off');
% GABA plot
ha=subplot(2, 2, 1);
% find peak of GABA plot... plot residuals above this...
gabamin = min(real(GABAData(ii,plotbounds)));
gabamax = max(real(GABAData(ii,plotbounds)));
resmax = max(residg);
residg = residg + gabamin - resmax;
if strcmp(MRS_struct.p.target,'GABA')
plot(freq(freqbounds),GaussModel_area(GaussModelParam(ii,:),freq(freqbounds)),'r',...
freq(plotbounds),real(GABAData(ii,plotbounds)), 'b', ...
freq(freqbounds),residg,'k');
set(gca,'XLim',[2.6 3.6]);
elseif strcmp(MRS_struct.p.target,'GSH')
freqrange=MRS_struct.spec.freq(freqbounds);
plot(MRS_struct.spec.freq, MRS_struct.spec.diff(ii,:), freqrange, ...
FiveGaussModel(FiveGaussModelParam(ii,:), freqrange),freqrange, ...
FiveGaussModel(GSHGaussModelParam(ii,:), freqrange),freqrange,...
FiveGaussModel(NAAGaussModelParam(ii,:), freqrange),...
MRS_struct.spec.freq(freqbounds),residg);
set(gca,'XLim',[1.8 4.2]);
end
if(strcmpi(MRS_struct.p.vendor,'Siemens'))
legendtxt = regexprep(MRS_struct.gabafile{ii*2-1}, '_','-');
else
legendtxt = regexprep(MRS_struct.gabafile{ii}, '_','-');
end
title(legendtxt);
set(gca,'XDir','reverse');
%%%%From here on is cosmetic - adding labels (and deciding where to).
hgaba=text(3,gabamax/4,MRS_struct.p.target);
set(hgaba,'horizontalAlignment', 'center');
%determine values of GABA tail (below 2.8 ppm.
z=abs(MRS_struct.spec.freq-2.79);%2.75
upperbound=find(min(z)==z);
tailtop=max(real(GABAData(ii,upperbound:(upperbound+150))));
tailbottom=min(real(GABAData(ii,upperbound:(upperbound+150))));
hgabares=text(2.8,min(residg),'residual');
set(hgabares,'horizontalAlignment', 'left');
text(2.8,tailtop+gabamax/20,'data','Color',[0 0 1]);
text(2.8,tailbottom-gabamax/20,'model','Color',[1 0 0]);
set(gca,'YTick',[]);
set(gca,'Box','off');
set(gca,'YColor','white');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 2. Water Fit
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if strcmp(MRS_struct.p.Reference_compound,'H2O')
T1=20;
%estimate height and baseline from data
[maxinWater, watermaxindex]=max(real(WaterData(ii,:)),[],2);
waterbase = mean(real(WaterData(1:500))); % avg
%Philips data do not phase well based on first point, so do a preliminary
%fit, then adjust phase of WaterData accordingly
if(strcmpi(MRS_struct.p.vendor,'Philips'))
%Run preliminary Fit of data
LGModelInit = [maxinWater 20 4.7 0.0 waterbase -50 ]; %works
lblg = [0.01*maxinWater 1 4.6 0 0 -50 ];
ublg = [40*maxinWater 100 4.8 0.000001 1 0 ];
%Fit from 5.6 ppm to 3.8 ppm RE 110826
z=abs(MRS_struct.spec.freq-5.6);
waterlow=find(min(z)==z);
z=abs(MRS_struct.spec.freq-3.8);
waterhigh=find(min(z)==z);
freqbounds=waterlow:waterhigh;
% Do the water fit (Lorentz-Gauss)
nlinopts = statset('nlinfit');
nlinopts = statset(nlinopts, 'MaxIter', 1e5);
[LGModelParam(ii,:),residw] = nlinfit(freq(freqbounds), real(WaterData(ii,freqbounds)),...
@(xdummy,ydummy) LorentzGaussModel(xdummy,ydummy),...
LGModelInit, nlinopts);
residw = -residw;
%Then use this for phasing
Eerror=zeros([120 1]);
for jj=1:120
Data=WaterData(ii,freqbounds)*exp(1i*pi/180*jj*3);
Model=LorentzGaussModel(LGModelParam(ii,:),freq(freqbounds));
Eerror(jj)=sum((real(Data)-Model).^2);
end
[number index]=min(Eerror);
WaterData=WaterData*exp(1i*pi/180*index*3);
end
% x(1) = Amplitude of (scaled) Lorentzian
% x(2) = 1 / hwhm of Lorentzian (hwhm = half width at half max)
% x(3) = centre freq of Lorentzian
% x(4) = linear baseline amplitude
% x(5) = constant baseline amplitude
% x(6) = -1 / 2 * sigma^2 of gaussian
LGModelInit = [maxinWater 20 4.7 0 waterbase -50 ]; %works
lblg = [0.01*maxinWater 1 4.6 0 0 -50 ];
ublg = [40*maxinWater 100 4.8 0.000001 1 0 ];
%Fit from 5.6 ppm to 3.8 ppm RE 110826
z=abs(MRS_struct.spec.freq-5.6);
waterlow=find(min(z)==z);
z=abs(MRS_struct.spec.freq-3.8);
waterhigh=find(min(z)==z);
freqbounds=waterlow:waterhigh;
% Do the water fit (Lorentz-Gauss)
% 111209 Always do the LSQCURV fitting - to initialise
%Lorentz-Gauss Starters
options = optimset('lsqcurvefit');
options = optimset(options,'Display','off','TolFun',1e-10,'Tolx',1e-10,'MaxIter',10000);
[LGModelParam(ii,:),residual(ii), residw] = lsqcurvefit(@(xdummy,ydummy) ...
LorentzGaussModel(xdummy,ydummy),...
LGModelInit, freq(freqbounds),real(WaterData(ii,freqbounds)),...
lblg,ublg,options);
residw = -residw;
if(waterfit_method == FIT_NLINFIT)
LGModelInit = LGModelParam(ii,:); % CJE 4 Jan 12
% nlinfit options
nlinopts = statset('nlinfit');
nlinopts = statset(nlinopts, 'MaxIter', 1e5);
%This double fit doesn't seem to work too well with the GE
%data... dig a little deeper
LGPModelInit = [maxinWater 20 freq(watermaxindex) 0 waterbase -50 0];
%figure(7)
%plot(freq(freqbounds), real(WaterData(ii,freqbounds)),freq(freqbounds),LorentzGaussModelP(LGPModelInit,freq(freqbounds)))
%figure(8)
[LGPModelParam(ii,:),residw] = nlinfit(freq(freqbounds), real(WaterData(ii,freqbounds)),...
@(xdummy,ydummy) LorentzGaussModelP(xdummy,ydummy),...
LGPModelInit, nlinopts);
if(~strcmpi(MRS_struct.p.vendor,'GE')&&~strcmpi(MRS_struct.p.vendor,'Siemens'))
%remove phase and run again
WaterData(ii,:)=WaterData(ii,:)*exp(1i*LGPModelParam(ii,7));
LGPModelParam(ii,7)=0;
[LGPModelParam(ii,:),residw] = nlinfit(freq(freqbounds), real(WaterData(ii,freqbounds)),...
@(xdummy,ydummy) LorentzGaussModelP(xdummy,ydummy),...
LGPModelParam(ii,:), nlinopts);
end
residw = -residw;
end
MRS_struct.out.WaterModelParam(ii,:) = LGPModelParam(ii,:);
hb=subplot(2, 2, 3);
waterheight = LGPModelParam(ii,1);
watmin = min(real(WaterData(ii,:)));
watmax = max(real(WaterData(ii,:)));
resmax = max(residw);
MRS_struct.out.WaterFitError(ii) = 100 * std(residw) / waterheight; %raee changed to residw
residw = residw + watmin - resmax;
stdevresidw=std(residw);
MRS_struct.out.GABAIU_Error_w = (MRS_struct.out.GABAFitError .^ 2 + ...
MRS_struct.out.WaterFitError .^ 2 ) .^ 0.5;
plot(freq(freqbounds),real(LorentzGaussModelP(LGPModelParam(ii,:),freq(freqbounds))), 'r', ...
freq(freqbounds),real(WaterData(ii,freqbounds)),'b', ...
freq(freqbounds), residw, 'k');
set(gca,'XDir','reverse');
set(gca,'YTick',[]);
set(gca,'Box','off');
set(gca,'YColor','white');
xlim([4.2 5.2]);
%Add on some labels
hwat=text(4.8,watmax/2,'Water');
set(hwat,'horizontalAlignment', 'right');
%Get the right vertical offset for the residual label
z=abs(freq(freqbounds)-4.4);
waterrlow=find(min(z)==z);
z=abs(freq(freqbounds)-4.25);
waterrhigh=find(min(z)==z);
rlabelbounds=waterrlow:waterrhigh;
labelfreq=freq(freqbounds);
axis_bottom=axis;
hwatres=text(4.4,max(min(residw(rlabelbounds))-0.05*watmax,axis_bottom(3)),'residual');
set(hwatres,'horizontalAlignment', 'left');
%CJE fixes water baseline code - baseline model as before...
WaterArea(ii)=sum(real(LorentzGaussModel(LGModelParam(ii,:),freq(freqbounds))) ...
- BaselineModel(LGModelParam(ii,3:5),freq(freqbounds)),2);
% convert watersum to integral
MRS_struct.out.WaterArea(ii)=WaterArea(ii) * (freq(1) - freq(2));
%MRS_struct.H20 = MRS_struct.out.WaterArea(ii) ./ std(residw); %This line doesn't make sense - commenting pending delete. RE
%generate scaled spectrum (for plotting) CJE Jan2011
MRS_struct.spec.diff_scaled(ii,:) = MRS_struct.spec.diff(ii,:) .* ...
repmat((1 ./ MRS_struct.out.WaterArea(ii)), [1 32768]);
%Concentration of GABA to water determined here.
[MRS_struct]=MRSGABAinstunits(MRS_struct, ii);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 3. Cr Fit
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Cr_OFF=MRS_struct.spec.off(ii,:);
%Fit CHo and Cr
ChoCrFitLimLow=2.6;
ChoCrFitLimHigh=3.6;
%Still need ranges for Creatine align plot
z=abs(MRS_struct.spec.freq-ChoCrFitLimHigh);
cclb=find(min(z)==z);
z=abs(MRS_struct.spec.freq-ChoCrFitLimLow);
ccub=find(min(z)==z);
freqrangecc=MRS_struct.spec.freq(cclb:ccub);
%Do some detective work to figure out the initial parameters
ChoCrMeanSpec = Cr_OFF(cclb:ccub).';
Baseline_offset=real(ChoCrMeanSpec(1)+ChoCrMeanSpec(end))/2;
Width_estimate=0.05;%ppm
Area_estimate=(max(real(ChoCrMeanSpec))-min(real(ChoCrMeanSpec)))*Width_estimate*4;
ChoCr_initx = [ Area_estimate Width_estimate 3.02 0 Baseline_offset 0 1].*[1 (2*MRS_struct.p.LarmorFreq) MRS_struct.p.LarmorFreq (180/pi) 1 1 1];
ChoCrMeanSpecFit(ii,:) = FitChoCr(freqrangecc, ChoCrMeanSpec, ChoCr_initx,MRS_struct.p.LarmorFreq);
MRS_struct.out.ChoCrMeanSpecFit(ii,:) = ChoCrMeanSpecFit(ii,:)./[1 (2*MRS_struct.p.LarmorFreq) MRS_struct.p.LarmorFreq (180/pi) 1 1 1];
%Initialise fitting pars
z=abs(MRS_struct.spec.freq-3.12);
lb=find(min(z)==z);
z=abs(MRS_struct.spec.freq-2.72);
ub=find(min(z)==z);
Cr_initx = [max(real(Cr_OFF(lb:ub))) 0.05 3.0 0 0 0 ];
freqrange = MRS_struct.spec.freq(lb:ub);
%Then use the same function as the Cr Fit in GannetLoad
nlinopts=statset('nlinfit');
nlinopts = statset(nlinopts, 'MaxIter', 1e5, 'Display','Off');
[CrFitParams(ii,:), residCr] = nlinfit(freqrange, real(Cr_OFF(lb:ub)), ...
@(xdummy, ydummy) LorentzModel(xdummy, ydummy),Cr_initx, nlinopts);
Crheight = CrFitParams(ii,1);
Crmin = min(real(Cr_OFF(lb:ub)));
Crmax = max(real(Cr_OFF(lb:ub)));
resmaxCr = max(residCr);
stdresidCr = std(residCr);
MRS_struct.out.CrFitError(ii) = 100 * stdresidCr / Crheight;
MRS_struct.out.GABAIU_Error_cr(ii) = (MRS_struct.out.GABAFitError(ii) .^ 2 + ...
MRS_struct.out.CrFitError(ii) .^ 2 ) .^ 0.5;
%MRS_struct.out.CrArea(ii)=sum(real(LorentzModel(CrFitParams(ii,:),freqrange)-LorentzModel([0 CrFitParams(ii,2:end)],freqrange))) * (freq(1) - freq(2));
MRS_struct.out.CrArea(ii)=sum(real(TwoLorentzModel([MRS_struct.out.ChoCrMeanSpecFit(ii,1:(end-1)) 0],freqrangecc)-TwoLorentzModel([0 MRS_struct.out.ChoCrMeanSpecFit(ii,2:(end-1)) 0],freqrangecc))) * (freq(1) - freq(2));
MRS_struct.out.ChoArea(ii)=sum(real(TwoLorentzModel([MRS_struct.out.ChoCrMeanSpecFit(ii,1:(end))],freqrangecc)-TwoLorentzModel([MRS_struct.out.ChoCrMeanSpecFit(ii,1:(end-1)) 0],freqrangecc))) * (freq(1) - freq(2));
MRS_struct.out.GABAconcCr(ii)=MRS_struct.out.GABAArea(ii)./MRS_struct.out.CrArea(ii);
MRS_struct.out.GABAconcCho(ii)=MRS_struct.out.GABAArea(ii)./MRS_struct.out.ChoArea(ii);
%alter resid Cr for plotting.
residCr = residCr + Crmin - resmaxCr;
if strcmp(MRS_struct.p.Reference_compound,'H2O')
%Plot the Cr fit
h2=subplot(2, 2, 4);
%debugging changes
plot(freqrangecc,real(TwoLorentzModel(MRS_struct.out.ChoCrMeanSpecFit(ii,:),freqrangecc)), 'r', ...
freqrangecc,real(TwoLorentzModel([MRS_struct.out.ChoCrMeanSpecFit(ii,1:(end-1)) 0],freqrangecc)), 'r', ...
MRS_struct.spec.freq,real(Cr_OFF(:)),'b', ...
freqrange, residCr, 'k');
set(gca,'XDir','reverse');
set(gca,'YTick',[],'Box','off');
xlim([2.6 3.6]);
set(gca,'YColor','white');
hcr=text(2.94,Crmax*0.75,'Creatine');
set(hcr,'horizontalAlignment', 'left')
%Transfer Cr plot into insert
subplot(2,2,3)
[h_m h_i]=inset(hb,h2);
set(h_i,'fontsize',6);
insert=get(h_i,'pos');
axi=get(hb,'pos');
set(h_i,'pos',[axi(1)+axi(3)-insert(3) insert(2:4)]);
%Add labels
hwat=text(4.8,watmax/2,'Water');
set(hwat,'horizontalAlignment', 'right')
set(h_m,'YTickLabel',[]);
set(h_m,'XTickLabel',[]);
set(gca,'Box','off')
set(gca,'YColor','white');
else
%Plot the Cr fit
hb=subplot(2, 2, 3);
%debugging changes
%plot(freqrange,real(LorentzModel(CrFitParams(ii,:),freqrange)), 'r', ...
% MRS_struct.spec.freq,real(Cr_OFF(:)),'b', ...
% freqrange, residCr, 'k');
plot(freqrangecc,real(TwoLorentzModel(MRS_struct.out.ChoCrMeanSpecFit(ii,:),freqrangecc)), 'r', ...
freqrangecc,real(TwoLorentzModel([MRS_struct.out.ChoCrMeanSpecFit(ii,1:(end-1)) 0],freqrangecc)), 'r', ...
MRS_struct.spec.freq,real(Cr_OFF(:)),'b', ...
freqrange, residCr, 'k');
set(gca,'XDir','reverse');
set(gca,'YTick',[]);
xlim([2.6 3.6]);
z=abs(freq(lb:ub)-3.12);
crlow=find(min(z)==z);
z=abs(freq(lb:ub)-2.9);
crhigh=find(min(z)==z);
crlabelbounds=crlow:crhigh;
hcres=text(3.12,max(residCr(crlabelbounds))+0.05*Crmax,'residual');
set(hcres,'horizontalAlignment', 'left');
hcdata=text(2.8,0.3*Crmax,'data','Color',[0 0 1]);
hcmodel=text(2.8,0.2*Crmax,'model','Color',[1 0 0]);
text(2.94,Crmax*0.75,'Creatine');
end
% GABA fitting information
if(strcmp(MRS_struct.p.AlignTo,'no')~=1)
tmp2 = '1';
else
tmp2 = '0';
end
if fit_method == FIT_NLINFIT
tmp3 = 'NLINFIT, ';
else
tmp3 = 'LSQCURVEFIT, ';
end
if waterfit_method == FIT_NLINFIT
tmp4 = [tmp3 'NLINFIT'];
else
tmp4 = [tmp3 'LSQCURVEFIT' ];
end
%and running the plot
if any(strcmp('mask',fieldnames(MRS_struct))) == 1
h=subplot(2,2,2);
p = get(h,'pos'); % get position of axes
set(h,'pos',[0.52 0.52 0.42 0.42]) % move the axes slightly
input=MRS_struct.mask.img(MRS_struct.ii,:,1:round(size(MRS_struct.mask.img,3)/3));
imagesc(squeeze(MRS_struct.mask.img(MRS_struct.ii,:,1:round(size(MRS_struct.mask.img,3)/3))));
colormap('gray');
caxis([0 1])
axis equal;
axis tight;
axis off;
subplot(2,2,4,'replace')
else
subplot(2,2,2)
end
axis off
if strcmp(MRS_struct.p.vendor,'Siemens')
tmp = [ 'filename : ' MRS_struct.gabafile{ii*2-1} ];
else
tmp = [ 'filename : ' MRS_struct.gabafile{ii} ];
end
tmp = regexprep(tmp, '_','-');
text(0,0.9, tmp, 'FontName', 'Helvetica');
if isfield(MRS_struct.p,'voxsize')
tmp = [ num2str(MRS_struct.p.Navg(ii)) ' averages of a ' num2str(MRS_struct.p.voxsize(ii,1)*MRS_struct.p.voxsize(ii,2)*MRS_struct.p.voxsize(ii,3)*.001) ' ml voxel'];
else
tmp = [ num2str(MRS_struct.p.Navg(ii)) ' averages'];
end
text(0,0.8, tmp, 'FontName', 'Helvetica');
%Remove this - more useful to add in Cr fWHM at a later date
%tmp = sprintf('GABA+ FWHM : %.2f Hz', MRS_struct.out.GABAFWHM(ii) );
%text(0,0.7, tmp);
if isfield(MRS_struct.p,'voxsize')
SNRfactor=round(sqrt(MRS_struct.p.Navg(ii))*MRS_struct.p.voxsize(ii,1)*MRS_struct.p.voxsize(ii,2)*MRS_struct.p.voxsize(ii,3)*.001);
tmp = ['SNR factor : ' num2str(SNRfactor)];
text(0,0.7, tmp, 'FontName', 'Helvetica');
end
tmp = sprintf('GABA+ Area : %.3g', MRS_struct.out.GABAArea(ii) );
text(0,0.6, tmp);
if strcmp(MRS_struct.p.Reference_compound,'H2O')
tmp = sprintf('H2O/Cr Area : %.3g/%.3g ', MRS_struct.out.WaterArea(ii),MRS_struct.out.CrArea(ii) );
text(0,0.5, tmp, 'FontName', 'Helvetica');
tmp = sprintf('%.1f, %.1f ', MRS_struct.out.GABAIU_Error_w(ii), MRS_struct.out.GABAIU_Error_cr(ii));
tmp = [tmp '%'];
tmp = ['FitErr (H/Cr) : ' tmp];
text(0,0.4, tmp, 'FontName', 'Helvetica');
tmp = [MRS_struct.p.target sprintf( '/H_2O : %.3f inst. units.', MRS_struct.out.GABAconciu(ii) )];
text(0,0.3, tmp, 'FontName', 'Helvetica');
tmp = [ MRS_struct.p.target sprintf('+/Cr i.r.: %.3f', MRS_struct.out.GABAconcCr(ii) )];
text(0,0.2, tmp, 'FontName', 'Helvetica');
tmp = [ 'Ver(Load/Fit): ' MRS_struct.versionload ',' MRS_struct.versionfit];
text(0,0.1, tmp, 'FontName', 'Helvetica');
%tmp = [MRS_struct.p.target ', Water fit alg. :' tmp4 ];
%text(0,-0.1, tmp, 'FontName', 'Helvetica');
else
tmp = sprintf('Cr Area : %.4f', MRS_struct.out.CrArea(ii) );
text(0,0.5, tmp, 'FontName', 'Helvetica');
tmp = sprintf('FitError (Cr): %.2f%%', MRS_struct.out.GABAIU_Error_cr);
text(0,0.4, tmp, 'FontName', 'Helvetica');
tmp = [MRS_struct.p.target sprintf( '+/Cr i.r.: %.4f', MRS_struct.out.GABAconcCr(ii) )];
text(0,0.3, tmp, 'FontName', 'Helvetica');
tmp = [ 'Ver(Load/Fit): ' MRS_struct.versionload ',' tmp2 ',' MRS_struct.versionfit];
text(0,0.2, tmp, 'FontName', 'Helvetica');
%tmp = [MRS_struct.p.target ', Water fit alg. :' tmp4 ];
%text(0,0.0, tmp, 'FontName', 'Helvetica');
end
%Add Gannet logo
if any(strcmp('mask',fieldnames(MRS_struct))) == 1
subplot(2,2,4)
else
subplot(2,2,4,'replace')
end
axis off;
script_path=which('GannetFit');
Gannet_circle_white=[script_path(1:(end-12)) '/GANNET_circle_white.jpg'];
A_2=imread(Gannet_circle_white);
hax=axes('Position',[0.80, 0.05, 0.15, 0.15]);
image(A_2);axis off; axis square;
%%%% Save EPS %%%%%
if strcmp(MRS_struct.p.vendor,'Siemens')
pfil_nopath = MRS_struct.gabafile{ii*2-1};
else
pfil_nopath = MRS_struct.gabafile{ii};
end
%for philips .data
if(strcmpi(MRS_struct.p.vendor,'Philips_data'))
fullpath = MRS_struct.gabafile{ii};
% fullpath = regexprep(fullpath, '\./', ''); NP edit out.
% see below
% fullpath = regexprep(fullpath, '/', '_');
fullpath = regexprep(fullpath, '.data', '_data');
fullpath = regexprep(fullpath, '\', '_');
fullpath = regexprep(fullpath, '/', '_');
%NP edit 02012013
%Previous code somehow didn't run when running from hierarchical
%folder (e.g. GABA_file = '.\name\MRI\raw.data) I got an error when Gannet tried to save the pdf for
%.data file. E.g. ??? Error using ==> saveas at 115 Invalid or missing path: ./MRSfit_140102/.\7011-0124\MRI\raw_008.data.pdf
%So it obviously didn't rewrite the path properly for the pdf here, but it IS important to get both folder and filename
%as a lot of the .data files have similar names (e.g.
%%raw_001.data). This change works for me for now, might not
%%be most elegant
end
tmp = strfind(pfil_nopath,'/');
tmp2 = strfind(pfil_nopath,'\');
if(tmp)
lastslash=tmp(end);
elseif (tmp2)
%maybe it's Windows...
lastslash=tmp2(end);
else
% it's in the current dir...
lastslash=0;
end
if(strcmpi(MRS_struct.p.vendor,'Philips'))
tmp = strfind(pfil_nopath, '.sdat');
tmp1= strfind(pfil_nopath, '.SDAT');
if size(tmp,1)>size(tmp1,1)
dot7 = tmp(end); % just in case there's another .sdat somewhere else...
else
dot7 = tmp1(end); % just in case there's another .sdat somewhere else...
end
elseif(strcmpi(MRS_struct.p.vendor,'GE'))
tmp = strfind(pfil_nopath, '.7');
dot7 = tmp(end); % just in case there's another .7 somewhere else...
elseif(strcmpi(MRS_struct.p.vendor,'Philips_data'))
tmp = strfind(pfil_nopath, '.data');
dot7 = tmp(end); % just in case there's another .data somewhere else...
elseif(strcmpi(MRS_struct.p.vendor,'Siemens'))
tmp = strfind(pfil_nopath, '.rda');
dot7 = tmp(end); % just in case there's another .data somewhere else...
elseif(strcmpi(MRS_struct.p.vendor,'Siemens_twix'))
tmp = strfind(pfil_nopath, '.dat');
dot7 = tmp(end); % just in case there's another .dat somewhere else...
end
pfil_nopath = pfil_nopath( (lastslash+1) : (dot7-1) );
if sum(strcmp(listfonts,'Helvetica'))>0
set(findall(h,'type','text'),'FontName','Helvetica')
set(ha,'FontName','Helvetica')
set(hb,'FontName','Helvetica')
end
%Save pdf output
set(gcf, 'PaperUnits', 'inches');
set(gcf,'PaperSize',[11 8.5]);
set(gcf,'PaperPosition',[0 0 11 8.5]);
if(strcmpi(MRS_struct.p.vendor,'Philips_data'))
pdfname=[ epsdirname '/' fullpath '.pdf' ];
else
pdfname=[ epsdirname '/' pfil_nopath '.pdf' ];
end
%epsdirname
if(exist(epsdirname,'dir') ~= 7)
epsdirname
mkdir(epsdirname)
end
saveas(gcf, pdfname);
if(ii==numscans)
if((MRS_struct.p.mat) == 1)
if(strcmpi(MRS_struct.p.vendor,'Philips_data'))
matname=[ epsdirname '/' 'MRS_struct' '.mat' ];
else
matname =[ epsdirname '/' 'MRS_struct' '.mat' ];
end
save(matname,'MRS_struct');
end
end
%140116: ADH reorder structure
if(isfield(MRS_struct, 'mask') == 1)
if(isfield(MRS_struct, 'waterfile') == 1)
structorder = {'versionload', 'versionfit', 'ii', ...
'gabafile', 'waterfile', 'p', 'fids', 'spec', 'out', 'mask'};
else
structorder = {'versionload', 'versionfit','ii', ...
'gabafile', 'p', 'fids', 'spec', 'out', 'mask'};
end
else
if(isfield(MRS_struct, 'waterfile') == 1)
structorder = {'versionload', 'versionfit', 'ii', ...
'gabafile', 'waterfile', 'p', 'fids', 'spec', 'out'};
else
structorder = {'versionload', 'versionfit','ii', ...
'gabafile', 'p', 'fids', 'spec', 'out'};
end
end
MRS_struct = orderfields(MRS_struct, structorder);
% Dec 09: based on FitSeries.m: Richard's GABA Fitting routine
% Fits using GaussModel
% Feb 10: Change the quantification method for water. Regions of poor homogeneity (e.g. limbic)
% can produce highly asymetric lineshapes, which are fitted poorly. Don't fit - integrate
% the water peak.
% March 10: 100301
% use MRS_struct to pass loaded data data, call MRSGABAinstunits from here.
% scaling of fitting to sort out differences between original (RE) and my analysis of FEF data
% change tolerance on gaba fit
% 110308: Keep definitions of fit functions in MRSGABAfit, rather
% than in separate .m files
% Ditto institutional units calc
% Include FIXED version of Lorentzian fitting
% Get Navg from struct (need version 110303, or later of
% MRSLoadPfiles
% rejig the output plots - one fig per scan.
% 110624: set parmeter to choose fitting routine... for awkward spectra
% report fit error (100*stdev(resid)/gabaheight), rather than "SNR"
% can estimate this from confidence interval for nlinfit - need
% GABA and water estimates
% 111111: RAEE To integrate in Philips data, which doesn't always have
% water spectr, we need to add in referenceing to Cr... through
% MRS_struct.p.Reference_compound
% 140115: MRS_struct.p.Reference_compound is now
% MRS_struct.p.Reference compound
%
%111214 integrating CJE's changes on water fitting (pre-init and revert to
%linear bseline). Also investigating Navg(ii)
end
% end of MRSGABAfit
%%%%%%%%%%%%%%%%%%%%%%%% GAUSS MODEL %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function F = GaussModel_area(x,freq)
% x(1) = gaussian amplitude
% x(2) = 1/(2*sigma^2)
% x(3) = centre freq of peak
% x(4) = amplitude of linear baseline
% x(5) = constant amplitude offset
%F = x(1)*sqrt(-x(2)/pi)*exp(x(2)*(freq-x(3)).*(freq-x(3)))+x(4)*(freq-x(3))+x(5);
F = x(1)*exp(x(2)*(freq-x(3)).*(freq-x(3)))+x(4)*(freq-x(3))+x(5);
%%%%%%%%%%%%%%%% OLD LORENTZGAUSSMODEL %%%%%%%%%%%%%%%%%%%%
%function F = LorentzGaussModel(x,freq)
%Lorentzian Model multiplied by a Gaussian. gaussian width determined by
%x(6). x(7) determines phase.
%F = ((ones(size(freq))./(x(2)^2*(freq-x(3)).*(freq-x(3))+1)*x(1))*cos(x(7))+(ones(size(freq))./(x(2)^2*(freq-x(3)).*(freq-x(3))+1)*x(2).*(freq-x(3)))*sin(x(7))).*(exp(x(6)*(freq-x(3)).*(freq-x(3))))+x(4)*(freq-x(3))+x(5);
%%%%%%%%%%%%%%%% LORENTZGAUSSMODEL %%%%%%%%%%%%%%%%%%%%
function F = LorentzGaussModel(x,freq)
% CJE 24Nov10 - removed phase term from fit - this is now dealt with
% by the phasing of the water ref scans in MRSLoadPfiles
%Lorentzian Model multiplied by a Gaussian.
% x(1) = Amplitude of (scaled) Lorentzian
% x(2) = 1 / hwhm of Lorentzian (hwhm = half width at half max)
% x(3) = centre freq of Lorentzian
% x(4) = linear baseline slope
% x(5) = constant baseline amplitude
% x(6) = -1 / 2 * sigma^2 of gaussian
% Lorentzian = (1/pi) * (hwhm) / (deltaf^2 + hwhm^2)
% Peak height of Lorentzian = 4 / (pi*hwhm)
% F is a normalised Lorentzian - height independent of hwhm
% = Lorentzian / Peak
%F =((ones(size(freq))./(x(2)^2*(freq-x(3)).*(freq-x(3))+1)*x(1))*cos(x(7))+(ones(size(freq))./(x(2)^2*(freq-x(3)).*(freq-x(3))+1)*x(2).*(freq-x(3)))*sin(x(7))).*(exp(x(6)*(freq-x(3)).*(freq-x(3))))+x(4)*(freq-x(3))+x(5);
% remove phasing
F = (x(1)*ones(size(freq))./(x(2)^2*(freq-x(3)).*(freq-x(3))+1)) ...
.* (exp(x(6)*(freq-x(3)).*(freq-x(3)))) ... % gaussian
+ x(4)*(freq-x(3)) ... % linear baseline
+x(5); % constant baseline
%%%%%%%%%%%%%%%% NEW LORENTZGAUSSMODEL WITH PHASE%%%%%%%%%%%%%%%%%%%%
function F = LorentzGaussModelP(x,freq)
% CJE 24Nov10 - removed phase term from fit - this is now dealt with
% by the phasing of the water ref scans in MRSLoadPfiles
%Lorentzian Model multiplied by a Gaussian.
% x(1) = Amplitude of (scaled) Lorentzian
% x(2) = 1 / hwhm of Lorentzian (hwhm = half width at half max)
% x(3) = centre freq of Lorentzian
% x(4) = linear baseline slope
% x(5) = constant baseline amplitude
% x(6) = -1 / 2 * sigma^2 of gaussian
% x(7) = phase (in rad)
% Lorentzian = (1/pi) * (hwhm) / (deltaf^2 + hwhm^2)
% Peak height of Lorentzian = 4 / (pi*hwhm)
% F is a normalised Lorentzian - height independent of hwhm
% = Lorentzian / Peak
%F =((ones(size(freq))./(x(2)^2*(freq-x(3)).*(freq-x(3))+1)*x(1))*cos(x(7))+(ones(size(freq))./(x(2)^2*(freq-x(3)).*(freq-x(3))+1)*x(2).*(freq-x(3)))*sin(x(7))).*(exp(x(6)*(freq-x(3)).*(freq-x(3))))+x(4)*(freq-x(3))+x(5);
% remove phasing
F = ((cos(x(7))*x(1)*ones(size(freq))+sin(x(7)*x(1)*x(2)*(freq-x(3))))./(x(2)^2*(freq-x(3)).*(freq-x(3))+1)) ...
.* (exp(x(6)*(freq-x(3)).*(freq-x(3)))) ... % gaussian
+ x(4)*(freq-x(3)) ... % linear baseline
+x(5); % constant baseline
%%%%%%%%%%%%%%% BASELINE %%%%%%%%%%%%%%%%%%%%%%%
function F = BaselineModel(x,freq)
F = x(2)*(freq-x(1))+x(3);
%%%%%%%%%%%%%%%%%%% INST UNITS CALC %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [MRS_struct] = MRSGABAinstunits(MRS_struct,ii)
% function [MRS_struct] = MRSGABAinstunits(MRS_struct)
% Convert GABA and Water amplitudes to institutional units
% (pseudo-concentration in mmol per litre).
% March 10: use MRS_struct.
PureWaterConc = 55000; % mmol/litre
WaterVisibility = 0.65; % This is approx the value from Ernst, Kreis, Ross
EditingEfficiency = 0.5;
T1_GABA = 0.80 ; % "empirically determined"...! Gives same values as RE's spreadsheet
% ... and consistent with Cr-CH2 T1 of 0.8 (Traber, 2004)
%Not yet putting in measured GABA T1, but it is in the pipeline - 1.35ish
T2_GABA = 0.13; % from occipital Cr-CH2, Traber 2004
T2_GABA = 0.088; % from JMRI paper 2011 Eden et al.
T1_Water = 1.100; % average of WM and GM, estimated from Wansapura 1999
T2_Water = 0.095; % average of WM and GM, estimated from Wansapura 1999
MM=0.45; % MM correction: fraction of GABA in GABA+ peak. (In TrypDep, 30 subjects: 55% of GABA+ was MM)
%This fraction is platform and implementation dependent, base on length and
%shape of editing pulses and ifis Henry method.
%
TR=MRS_struct.p.TR/1000;
TE=MRS_struct.p.TE/1000;
N_H_GABA=2;
N_H_Water=2;
Nspectra = length(MRS_struct.gabafile);
%Nwateravg=8;
T1_factor = (1-exp(-TR./T1_Water)) ./ (1-exp(-TR./T1_GABA));
T2_factor = exp(-TE./T2_Water) ./ exp(-TE./T2_GABA);
if(strcmpi(MRS_struct.p.vendor,'Siemens'))
MRS_struct.out.GABAconciu(ii) = (MRS_struct.out.GABAArea(ii) ./ MRS_struct.out.WaterArea(ii)) ...
* PureWaterConc*WaterVisibility*T1_factor*T2_factor*(N_H_Water./N_H_GABA) ...
* MM /2.0 ./ EditingEfficiency; %Factor of 2.0 is appropriate for averaged data, read in separately as on and off (Siemens).
else
MRS_struct.out.GABAconciu(ii) = (MRS_struct.out.GABAArea(ii) ./ MRS_struct.out.WaterArea(ii)) ...
* PureWaterConc*WaterVisibility*T1_factor*T2_factor*(N_H_Water./N_H_GABA) ...
* MM ./ EditingEfficiency;
end
FAC=PureWaterConc*WaterVisibility*(N_H_Water./N_H_GABA) ...
* MM ./ EditingEfficiency*T1_factor*T2_factor;
%%%%%%%%%%%%%%% INSET FIGURE %%%%%%%%%%%%%%%%%%%%%%%
function [h_main, h_inset]=inset(main_handle, inset_handle,inset_size)
% The function plotting figure inside figure (main and inset) from 2 existing figures.
% inset_size is the fraction of inset-figure size, default value is 0.35
% The outputs are the axes-handles of both.
%
% An examle can found in the file: inset_example.m
%
% Moshe Lindner, August 2010 (C).
if nargin==2
inset_size=0.35;
end
inset_size=inset_size*.5;
%figure
new_fig=gcf;
main_fig = findobj(main_handle,'Type','axes');
h_main = copyobj(main_fig,new_fig);
set(h_main,'Position',get(main_fig,'Position'))
inset_fig = findobj(inset_handle,'Type','axes');
h_inset = copyobj(inset_fig,new_fig);
ax=get(main_fig,'Position');
set(h_inset,'Position', [1.3*ax(1)+ax(3)-inset_size 1.001*ax(2)+ax(4)-inset_size inset_size*0.7 inset_size*0.9])