update SNR calculations

+Segmentation/PerformSegmentation.m

@@ -179,7 +179,7 @@
             case 'Ventilation'                            
                switch MainInput.SliceOrientation
                     case 'coronal' 
-                        if MainInput.NoProtonImage == 0 && strcmp(MainInput.Imagestosegment, 'Xe & Proton Registered') == 1
+                        if MainInput.NoProtonImage == 0 && strcmp(MainInput.Imagestosegment, 'Proton & Xe Registered') == 1
                             SegmentType = 'vent_2D_2ch_cor'; %system('predict_mask_2DVent_w_H_coronal.exe')
                         elseif strcmp(MainInput.Imagestosegment, 'Xenon') == 1
                             SegmentType = 'vent_2D_1ch_cor'; 

+VentilationFunctions/calculate_SNR.m

@@ -54,12 +54,12 @@
 %     airwaymask = Segmentation.SegmentLungthresh(MR,1,1);
 % end
 % force airway mask
-airwaymask = Segmentation.SegmentLungthresh(MR,0.5,1);
+airwaymask = Segmentation.SegmentLungthresh(MR,1,0.3);
 % airwaymask = double(MR > 2000);
-% imslice(backgroundmask)
+
 backgroundmask = double(imcomplement(maskarray_dilated).*~airwaymask);
 background1 = (MR).*(backgroundmask);
-
+% imslice(backgroundmask)
 % % Label 0s in the background noise array as NaNs
 % background1(background1 == 0) = NaN;
 % 
@@ -109,8 +109,8 @@
         mean_noise(isnan(mean_noise))=0;
         std_noise(isnan(std_noise))=0;
 
-        SNR_slice(n) = round(signal_n_avg(n) / std_noise(n),2)*sqrt(2 - (pi/2)); %signal to noise ratio
-        SNRvv_slice(n) = round(signalvv_avg(n) / std_noise(n),2)*sqrt(2 - (pi/2)); %signal to noise ratio
+        SNR_slice(n) = round((signal_n_avg(n) - mean_noise(n)) / std_noise(n),2)*sqrt(2 - (pi/2)); %signal to noise ratio
+        SNRvv_slice(n) = round((signalvv_avg(n) - mean_noise(n)) / std_noise(n),2)*sqrt(2 - (pi/2)); %signal to noise ratio
 end
 SNR_slice(isnan(SNR_slice))=0;
 SNR_slice(isinf(SNR_slice)) = 0;

+VentilationFunctions/calculate_VDP_CCHMC.m

@@ -14,9 +14,10 @@
 
 %% VDP Calculation Code:
 MR = Ventilation.Image;
-maskarray = double(Ventilation.LungMask + Ventilation.VesselMask);
-maskarray(maskarray > 1) = 0;
-maskarray = double(maskarray);
+maskarray = double(Ventilation.LungMask);
+% maskarray = double(Ventilation.LungMask + Ventilation.VesselMask);
+% maskarray(maskarray > 1) = 0;
+% maskarray = double(maskarray);
 complete = Ventilation.CompleteThresh;
 incomplete = Ventilation.IncompleteThresh;
 hyper = Ventilation.HyperventilatedThresh;

+VentilationFunctions/calculate_VHI.m

@@ -22,9 +22,7 @@
 
     % Extract input data and define the effective binary mask
     image = Ventilation.Image;
-    maskarray = double(Ventilation.LungMask + Ventilation.VesselMask);
-    maskarray(maskarray > 1) = 0;  % Exclude overlapping regions
-    maskarray = double(maskarray);
+    maskarray = double(Ventilation.LungMask);
 
     [rows, cols, slices] = size(image);