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[Fix] Fixes in mcx config and brain-and-scalp recon #60

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[Fix] Fixes in mcx config and brain-and-scalp recon #60

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919dafe
fix adding more than 4 tissues to mcx cfg
mashayu Jul 13, 2023
1c07104
fix non-existent activeChIdxs in brain-and-scalp recon
mashayu Jul 13, 2023
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11 changes: 6 additions & 5 deletions ForwardModel/runMCXlab.m
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Original file line number Diff line number Diff line change
Expand Up @@ -249,11 +249,12 @@
cfg.isnormalized = 1;
cfg.outputtype = 'fluence';

cfg.prop=[ 0 0 1.0000 1.0000 % background/air
tiss_prop(1).absorption(iWav) tiss_prop(1).scattering(iWav) tiss_prop(1).anisotropy(1) tiss_prop(1).refraction(1)
tiss_prop(2).absorption(iWav) tiss_prop(2).scattering(iWav) tiss_prop(2).anisotropy(1) tiss_prop(2).refraction(1)
tiss_prop(3).absorption(iWav) tiss_prop(3).scattering(iWav) tiss_prop(3).anisotropy(1) tiss_prop(3).refraction(1)
tiss_prop(4).absorption(iWav) tiss_prop(4).scattering(iWav) tiss_prop(4).anisotropy(1) tiss_prop(4).refraction(1) ];
cfg.prop=[ 0 0 1.0000 1.0000 ]; % background/air
for i = 1:length(tiss_prop)
cfg.prop = [cfg.prop; ...
tiss_prop(i).absorption(iWav) tiss_prop(i).scattering(iWav) tiss_prop(i).anisotropy(1) tiss_prop(i).refraction(1)]

end

cfg.seed=floor(rand()*10e+7);
cfg.nphoton=num_phot;
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11 changes: 4 additions & 7 deletions ImgRecon/ImageRecon.m
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Expand Up @@ -283,13 +283,10 @@ function image_recon_Callback(~, ~, handles)
end

elseif value2 == 1 % brain and scalp reconstruction without short separation regression (Zhan2012)

Adot = Adot(activeChIdxs,:,:);
Adot = Adot(longSepChLst,:,:);

Adot_scalp = Adot_scalp(activeChIdxs,:,:);
Adot_scalp = Adot_scalp(longSepChLst,:,:);


Adot = Adot(activeChLst_SDpairs,:,:);
Adot_scalp = Adot_scalp(activeChLst_SDpairs,:,:);

% get alpha and beta for regularization
alpha = str2num(get(handles.alpha_brain_scalp,'String')); %#ok<*ST2NM>
beta = str2num(get(handles.beta_brain_scalp,'String'));
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