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GannetPlotPrePostAlign.m
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GannetPlotPrePostAlign.m
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function GannetPlotPrePostAlign(MRS_struct, vox, ii, kk)
% Plot pre-/post-alignment spectra
% Updates by MGSaleh 2016, MM 2017-2019
if MRS_struct.p.HERMES
SpectraToPlot = zeros(2*length(MRS_struct.p.target), length(MRS_struct.spec.(vox{kk}).(MRS_struct.p.target{1}).diff));
count = 0;
for jj = 1:length(MRS_struct.p.target)
SpectraToPlot((1:2)+count,:) = [MRS_struct.spec.(vox{kk}).(MRS_struct.p.target{jj}).diff(ii,:); ...
MRS_struct.spec.(vox{kk}).(MRS_struct.p.target{jj}).diff_noalign(ii,:)];
count = count + 2;
end
% Shift baselines to zero
baserange = MRS_struct.spec.freq <= 0 & MRS_struct.spec.freq >= -0.5;
% Some bandwidth-limited acquisitions may not record anything below
% 0 ppm, in this case get the baseline from the other side of
% water. (GO: 180213)
if sum(baserange) == 0
baserange = MRS_struct.spec.freq >= 7 & MRS_struct.spec.freq <= 8;
end
peakrange = zeros(length(MRS_struct.p.target), length(MRS_struct.spec.freq));
for jj = 1:length(MRS_struct.p.target)
switch MRS_struct.p.target{jj}
case {'GABA','Glx','GABAGlx'}
if MRS_struct.p.phantom
peakrange(jj,:) = MRS_struct.spec.freq <= 4.25 & MRS_struct.spec.freq >= 1.0;
else
peakrange(jj,:) = MRS_struct.spec.freq <= 4.1 & MRS_struct.spec.freq >= 2.26;
end
case 'GSH'
if ~MRS_struct.p.HERCULES
peakrange(jj,:) = MRS_struct.spec.freq <= 3.5 & MRS_struct.spec.freq >= 0.5;
else
peakrange(jj,:) = MRS_struct.spec.freq <= 4.25 & MRS_struct.spec.freq >= 3;
end
case {'Lac','EtOH'}
peakrange(jj,:) = MRS_struct.spec.freq <= 3 & MRS_struct.spec.freq >= 0.5;
end
end
specbaseline = mean(real(SpectraToPlot(:,baserange)),2);
SpectraToPlot = SpectraToPlot - repmat(specbaseline, [1 size(SpectraToPlot,2)]);
% Stack spectra
if MRS_struct.p.phantom
signalrange = max(max(real(SpectraToPlot(1:2,logical(peakrange(1,:)))))) - min(min(real(SpectraToPlot(1:2,logical(peakrange(1,:))))));
SpectraToPlot(3:4,:) = SpectraToPlot(3:4,:) + signalrange;
yaxismax = max(real(SpectraToPlot(3,logical(peakrange(2,:)))));
yaxismin = min(real(SpectraToPlot(1,logical(peakrange(1,:)))));
yrange = abs(yaxismax - yaxismin);
yaxismax = yaxismax + 0.1*yrange;
yaxismin = yaxismin - 0.1*yrange;
else
if all(ismember(MRS_struct.p.target,{'GABAGlx','GSH'})) || all(ismember(MRS_struct.p.target,{'GABA','GSH'}))
if ~MRS_struct.p.HERCULES
peakheight = abs(min(real(SpectraToPlot(3,logical(peakrange(2,:))))));
else
peakheight = abs(max(real(SpectraToPlot(1,logical(peakrange(1,:))))));
end
SpectraToPlot(3:4,:) = SpectraToPlot(3:4,:) + 1.5*peakheight;
yaxismax = max(real(SpectraToPlot(3,logical(peakrange(2,:)))));
yaxismin = min(real(SpectraToPlot(1,logical(peakrange(1,:)))));
yrange = abs(yaxismax - yaxismin);
yaxismax = yaxismax + 0.1*yrange;
yaxismin = yaxismin - 0.1*yrange;
elseif all(ismember(MRS_struct.p.target,{'EtOH','GABA','GSH'}))
peakheight = abs(min(real(SpectraToPlot(5,logical(peakrange(3,:))))));
SpectraToPlot(5:6,:) = SpectraToPlot(5:6,:) + 1.5*peakheight;
peakheight = abs(max(real(SpectraToPlot(1,logical(peakrange(1,:))))));
SpectraToPlot(1:2,:) = SpectraToPlot(1:2,:) - 1.5*peakheight;
yaxismax = abs(max(real(SpectraToPlot(5,logical(peakrange(3,:))))));
yaxismax = yaxismax + 0.2*yaxismax;
yaxismin = max(real(SpectraToPlot(1,logical(peakrange(1,:)))));
yaxismin = yaxismin - 4*abs(yaxismin);
else
peakheight = abs(min(real(SpectraToPlot(5,logical(peakrange(3,:))))));
SpectraToPlot(5:6,:) = SpectraToPlot(5:6,:) + 1.5*peakheight;
end
end
count = 0;
for jj = 1:length(MRS_struct.p.target)
hold on;
plot(MRS_struct.spec.freq, real(SpectraToPlot(2+count*2,:)), 'Color', 'r');
plot(MRS_struct.spec.freq, real(SpectraToPlot(1+count*2,:)), 'Color', 'b');
hold off;
count = count + 1;
end
else
SpectraToPlot = [MRS_struct.spec.(vox{kk}).(MRS_struct.p.target{1}).diff(ii,:); ...
MRS_struct.spec.(vox{kk}).(MRS_struct.p.target{1}).diff_noalign(ii,:)];
% Shift baselines to zero
baserange = MRS_struct.spec.freq <= 0 & MRS_struct.spec.freq >= -0.5;
% Some bandwidth-limited acquisitions may not record anything below
% 0 ppm, in this case get the baseline from the other side of
% water. (GO: 180213)
if sum(baserange) == 0
baserange = MRS_struct.spec.freq >= 7 & MRS_struct.spec.freq <= 8;
end
switch MRS_struct.p.target{1}
case {'GABA','Glx','GABAGlx'}
peakrange = MRS_struct.spec.freq <= 4.1 & MRS_struct.spec.freq >= 2.26;
case 'GSH'
peakrange = MRS_struct.spec.freq <= 3.5 & MRS_struct.spec.freq >= 0.5;
case {'Lac','EtOH'}
peakrange = MRS_struct.spec.freq <= 3 & MRS_struct.spec.freq >= 0.5;
end
specbaseline = mean(real(SpectraToPlot(:,baserange)),2);
SpectraToPlot = SpectraToPlot - repmat(specbaseline, [1 length(SpectraToPlot)]);
% Stack spectra
peakheight = max(abs(real(SpectraToPlot(1,peakrange))));
SpectraToPlot(2,:) = SpectraToPlot(2,:) + peakheight + 0.05*peakheight;
hold on;
plot(MRS_struct.spec.freq, real(SpectraToPlot(2,:)), 'Color', 'r');
plot(MRS_struct.spec.freq, real(SpectraToPlot(1,:)), 'Color', 'b');
hold off;
yaxismax = max(max(real(SpectraToPlot(:,peakrange)),[],2));
yaxismin = min(min(real(SpectraToPlot(:,peakrange)),[],2));
yrange = abs(yaxismax - yaxismin);
yaxismax = yaxismax + 0.1*yrange;
if any(strcmp(MRS_struct.p.target{1}, {'GABA','Glx','GABAGlx'}))
yaxismin = yaxismin - 0.3*yrange;
else
yaxismin = yaxismin - 0.1*yrange;
end
end
if strcmp(MRS_struct.p.target{1},'EtOH')
legend({'pre','post'},'EdgeColor',[1 1 1],'Location','northwest');
else
legend({'pre','post'},'EdgeColor',[1 1 1]);
end
axis([0 5 yaxismin yaxismax]);
set(gca,'XDir','reverse','TickDir','out','box','off','XTick',0:5);
ax = get(gca,'YAxis');
set(ax,'Visible','off');
xlabel('ppm');
if MRS_struct.p.HERMES
title({'Edited Spectra';'(pre- and post-alignment)'});
else
title({'Edited Spectrum';'(pre- and post-alignment)'});
end