createADCmap.m

function createADCmap(dicom_list, vial_file, slice, TE_keep, b_keep)
    load([vial_file]); 
    imgeVials = imgeEPI; 
    geomInfoVials = geomInfo; 
    
    for f = 1:length(dicom_list)
        load([dicom_list{f} '.mat'], 'imge', 'imge_reg', 'geomInfo'); 
        if exist('imge_reg', 'var')
            imge = imge_reg; 
        end 
        
        % Pad slice dimension if image is 2D for reslicing
        if size(imge, 3) == 1
            if ndims(imge) == 4
                imge = repmat(imge,[1,1,2,1]); 
            elseif ndims(imge) == 5
                imge = imge(:,:,:,:,TE_keep);
                imge = repmat(imge,[1,1,2,1]);
            end
        end 
    
        % Resample to Vial Reference 
        imge_interp = coregister_images('linear', imgeVials, geomInfoVials, imge, geomInfo); 
         
    
        % Fit to ADC 
        %if ndims
        if strcmp(dicom_list{f}(1:3), 'SOS')
            b = [10, 50, 100, 840];
        else 
            b = [0, 50, 100, 800];
        end 
    
        % S is a 2D Slice of DWI data, all b-values
        S = squeeze(imge_interp(:,:,slice,b_keep)); 
        S2 = reshape(S, [size(S,1)*size(S,2), size(S,3)]);
    
        Y = log(S2./S2(:,1)); 
        X = b(b_keep);
        
        for p = 1:length(Y)
            P(p,:) = polyfit(X,Y(p,:),1); 
        end 
        ADC = -1*reshape(P(:,1), size(S,1:2))*1E3;
    
        figure; 
        sbp = tiledlayout(2,1, 'Padding', 'tight', 'TileSpacing', 'tight');
        ax1 = nexttile()
        imagesc(squeeze(imge_interp(:,:,slice,1))); axis image;  colormap(ax1, 'gray');
        ax2 = nexttile()
        imagesc(ADC); axis image;  colormap(ax2, 'jet'); clim([.2 2.25]); c = colorbar;
        c.FontSize = 14; 
        sgtitle(['ADC: ' strrep(dicom_list{f}, '_', ' ')]);
        saveas(gca, ['ADC_' dicom_list{f}], 'png')
        
    end 
end