How to create point cloud output masks from .mat files

Question

Tess 2025-2-13

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https://ww2.mathworks.cn/matlabcentral/answers/2174002-how-to-create-point-cloud-output-masks-from-mat-files

回答： Shantanu Dixit 2025-2-17

Hello,

I have been using the Matlab medical image labeler to segment hip mri scans. Currently, I am trying to download the segmented MRI images as PDFs where I can mask them and convert them to binary code. The main goal is to compare the binary code so I can compare different masks of the same hip scan and find the borders of the femur head. I am trying to write code that uses point cloud output masks; however, I am unsure how to get a ply file from the medical image labeler (as you can only export as a .mat file). I was wondering if anyone had any suggestions on how to successfully mask the segmented images or any different recommendations that I could use!

I appreciate any help or advice you can give.

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Answer 1

Shantanu Dixit 2025-2-17

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https://ww2.mathworks.cn/matlabcentral/answers/2174002-how-to-create-point-cloud-output-masks-from-mat-files#answer_1559913

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Hi Tess,

You can create point cloud output masks from .mat files by extracting the mask data and converting the data into 3D coordinates using 'ind2sub': https://www.mathworks.com/help/matlab/ref/ind2sub.html. Once the coordinates are extracted you can create a point cloud object using 'pointCloud': https://www.mathworks.com/help/vision/ref/pointcloud.html.

% Assuming data holds the .mat file information
mask = data.labelData;  % Accessing label information (replace with the actual name)
% Convert mask to 3d coordinate
[y, x, z] = ind2sub(size(mask), find(mask == Label)); % Replace Label with particular label ID
% scale the indices appropriately using the metadata (pixel spacing, position)
points = [x, y, z];  
% Create point cloud object
ptCloud = pointCloud(points);  