how to read in a curved region of interest that is one plane?

Hello,

I have a manually drawn a mask on an image that is curved where the red line is the mask, and the black is the the image with the signal; here are two examples:

In the middle of the image there will always be an area where when the mask is applied it will be zero. Additionally, there will always be zeros on boths of the outside of the mask.

here is and example of when it didn't work properly (you can see that there are a bunch of zeros in the middle):

I have been able to read and plot the corresponding values for a straight line (here is an example):

and here is an example of the plot:

and here is the function where I read in the ADC values:

ADC_size = size(ADC);
ROI_resampled = imresize3(ROI, ADC_size, 'nearest') > 0;

% Extract ADC and B0 values within the ROI
adcValues = ADC(ROI_resampled);

and here is the whole code for the plot:

            ADC_size = size(ADC);
            ROI_resampled = imresize3(ROI, ADC_size, 'nearest') > 0;

            % Extract ADC and B0 values within the ROI
            adcValues = ADC(ROI_resampled);
        
            % Find the longest sequence of zeros
            diffs = diff(zeroIndices);
            splitPoints = find(diffs > 1); % Gaps indicate separate zero groups

            if ~isempty(splitPoints)
                startIdx = zeroIndices(splitPoints(1) + 1); % Start of middle zero block
                endIdx = zeroIndices(splitPoints(end));     % End of middle zero block
            else
                startIdx = zeroIndices(1);
                endIdx = zeroIndices(end);
            end

            % Find the indices just outside the middle zero block
            indexAbove = startIdx - 1;
            indexBelow = endIdx + 1;

            % Ensure indices are within bounds
            if indexAbove < 1
                indexAbove = NaN;
            end
            if indexBelow > length(adcValues)
                indexBelow = NaN;
            end

            fprintf('Index above middle zeros: %d\n', indexAbove);
            fprintf('Index below middle zeros: %d\n', indexBelow);
            %% 
            
            % Use indexBelow as reference if available, otherwise indexAbove
            if ~isnan(indexBelow)
                referenceIndex = indexBelow;
            elseif ~isnan(indexAbove)
                referenceIndex = indexAbove;
            else
                error('No valid reference index found.');
            end
            
            %% 
            
            % Automatically assign distances in mm
            x_mm = zeros(size(adcValues)); % Initialize
            
            
            % Assign values above the middle zero block
            for i = indexAbove:-1:1
                x_mm(i) = x_mm(i+1) - voxel_size;
            end
            
            % Assign values below the middle zero block
            for i = indexBelow:length(adcValues)
                x_mm(i) = x_mm(i-1) + voxel_size;
            end
            
            
            % Flip the x-axis values
            x_mm_flipped = -x_mm;

            figure();
            plot(x_mm_flipped, adcValues);

Can you help me read line by line the masked values that are next to eachother?

Answer 1

[Matt J]

I don't quite understand what you are trying to do, but I have the vague impression you are trying to interpolate an image on a cross-sectional surface (marked by the red line). If so, you should look at the slice command, with particular attention to this example,

https://www.mathworks.com/help/releases/R2024b/matlab/ref/slice.html?searchPort=64988#mw_e9ea56fc-b860-4fbe-99d5-6c3e4725132f

and possibly also interp2, interp3, and, griddedInterpolant.