3D brain tumor segmentation using a two-stage optimal mass transport algorithm

Wen Wei Lin, Cheng Juang, Mei Heng Yueh, Tsung Ming Huang*, Tiexiang Li*, Sheng Wang, Shing Tung Yau


研究成果: 雜誌貢獻期刊論文同行評審

7 引文 斯高帕斯(Scopus)


Optimal mass transport (OMT) theory, the goal of which is to move any irregular 3D object (i.e., the brain) without causing significant distortion, is used to preprocess brain tumor datasets for the first time in this paper. The first stage of a two-stage OMT (TSOMT) procedure transforms the brain into a unit solid ball. The second stage transforms the unit ball into a cube, as it is easier to apply a 3D convolutional neural network to rectangular coordinates. Small variations in the local mass-measure stretch ratio among all the brain tumor datasets confirm the robustness of the transform. Additionally, the distortion is kept at a minimum with a reasonable transport cost. The original 240 × 240 × 155 × 4 dataset is thus reduced to a cube of 128 × 128 × 128 × 4 , which is a 76.6% reduction in the total number of voxels, without losing much detail. Three typical U-Nets are trained separately to predict the whole tumor (WT), tumor core (TC), and enhanced tumor (ET) from the cube. An impressive training accuracy of 0.9822 in the WT cube is achieved at 400 epochs. An inverse TSOMT method is applied to the predicted cube to obtain the brain results. The conversion loss from the TSOMT method to the inverse TSOMT method is found to be less than one percent. For training, good Dice scores (0.9781 for the WT, 0.9637 for the TC, and 0.9305 for the ET) can be obtained. Significant improvements in brain tumor detection and the segmentation accuracy are achieved. For testing, postprocessing (rotation) is added to the TSOMT, U-Net prediction, and inverse TSOMT methods for an accuracy improvement of one to two percent. It takes 200 seconds to complete the whole segmentation process on each new brain tumor dataset.

期刊Scientific reports
出版狀態已發佈 - 2021 12月

ASJC Scopus subject areas

  • 多學科


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