IMPORTANT: You are encouraged to read this entire file and make necessary modifications to your code before program execution.
MATLAB code for "A Framework for Automatic Morphological Feature Extraction and Analysis of Abdominal Organs in MRI Volumes".
by Hykoush A. Asaturyan, E. Louise Thomas, Jimmy D. Bell and Barbara Villarini.
Please see [https://tinyurl.com/vb3hb2b] for online access to PDF file.
This program was built using MATLAB R2017b and MATLAB R2018a, and employs the Image Processing Toolbox and Computer Vision Toolbox.
Purpose of project task:
Morphological feature extraction of segmented or annotated organs in radiological volumes (scans).
Purpose of program code for project task:
(1) Compute organ volume (volume);
(2) Compute organ global curvature (meanCurv);
(3) save to a MAT file: 3D rendered organ volume data (dataInterp), smoothed rendered 3D organ data (dataFilt), principal curvatures and directions (curvData), and values of volume (volume) and global curvature (meanCurv);
(4) save to a NIFTY file: 3D rendered organ volume data (dataFiltBin);
(5) save volume (volume) and curvature (meanCurv) results of each 3D rendered organ to a .xlsx file.
To execute the program, modify and run "VolumeCurvatureReconstruction.m".
IMPORTANT TO NOTE: Please modify the following variables below:
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resultsFolder = 'path-to-folder-that-stores-results';
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inputFolder = 'path-to-folder-that-contains-input-files-of-organ-segmentations-or-annotations';
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totalData = 'struct-listing-all-files-that-contain-3D-arrays-of-binary-organ-annotations';
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volSize = ['width', 'height', 'depth'] where 'width' is the number of columns in the binary organ-annotation array; 'height' is the number of rows in the binary organ-annotation array; and 'depth' is the number of slices (2D) in the binary organ-annotation array.
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interpVoxSize = ['x', 'y', 'z'] where 'x' is pixel interval in axial direction; 'y' is pixel interval in sagittal direction; 'z' is the spacing between each slice (2D) in the binary organ-annotation array.