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研究生: 蕭叡謙
Jui-Chien Hsiao
論文名稱: 雙注意力機制設計結合轉換器之深層特徵於磁振影像上的腦腫瘤切割方法
mMRI Brain Tumor Segmentation with Dual Attention UNet and Transformer Deep Feature Extractor
指導教授: 郭景明
Jing-Ming Guo
口試委員: 王乃堅
Nai-Jian Wang
陳彥霖
Yen-Lin Chen
李宗南
Chung-Nan Lee
徐繼聖
Gee-Sern Jison Hsu
學位類別: 碩士
Master
系所名稱: 電資學院 - 電機工程系
Department of Electrical Engineering
論文出版年: 2021
畢業學年度: 109
語文別: 中文
論文頁數: 83
中文關鍵詞: 腦部腫瘤切割自注意力機制深度監督
外文關鍵詞: Brain Tumor Segmentation, Transformer, Attention Mechanism
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本論文提出了一個以當前熱門主題Transformer及醫療影像常用的架構U-Net為基底的架構對多模態腦部腫瘤進行切割任務,並且在跳連結上加入了雙注意力機制以及在解碼器部分加入了深度監督以確保還原過程中的特徵最具有代表性並讓網路獲得更好的收斂效果。
本論文使用的資料集為BraTS2020,其中訓練集為369個樣本組成,驗證集 為125個樣本組成,對於驗證集官方並未提供相對應的切割標註,因此並不是作為模型挑選的資料集,而是需要上傳切割結果至CBICA IPP網站進行評分。
在前處理的部分,由於訓練樣本是由多台不同儀器取得,因此在像素值的
分布上為不同基準,故需要先對樣本進行Z-score Normalization將其標準化與切除樣本中極大極小值去除噪點。
在後處理的部分,由於訓練樣本中依據腫瘤嚴重程度分為HGG(High-grade Gliomas) 與 LGG(Low-grade gliomas),而其在腫瘤表現上有些許不同,最明顯的部分為部分LGG是沒有增強腫瘤的,這將會造成評分時的極端現象,dice分數非0即0,因此後處理在這個資料集是必須的,其中包含將面積小於10像素的聯通元件(connected component)去除與將面積小於500 像素的增強腫瘤更正為壞死區域或非增強腫瘤。


Medical image segmentation is a relatively tricky task compared to natural image semantic segmentation. The dataset size for medical image were usually small caused by the difficulty of data retrieval. In this paper, a UNet-like architecture is proposed and implemented on MICCAI BraTS 2020 dataset, which contains 369 training data and 125 validation data. The model performance will be evaluated based on online scoring of validation dataset provided by CBICA IPP.
The proposed UNet-like architecture incorporated Transformer encoder to strengthen high-level feature extraction. The shortage of Transformer on low-level feature was made up by the UNet decoder skip connection, on which we designed an attention mechanism to separate spatial and channel attention. We also utilized deep supervision technique to deeply supervise the decoder learning process for better feature extraction.
The proposed UNet-like architecture achieved dice score of 0.78345, 0.90402, 0.83887 on ET, WT, TC respectively given by CBICA IPP online evaluation, which is a competitive result and surpassed most of the similar approaches in MICCAI BraTS2020 Challenge.

摘要 I Abstract II 誌謝 III 目錄 IV 圖目錄 VI 表目錄 IX 第一章 緒論 1 1.1研究背景與動機 1 1.2自然影像與醫療影像的差異 2 1.3 論文架構 3 第二章 文獻探討 4 2.1 類神經網路相關文獻 4 2.1.1向前傳播(Forward Propagation) 5 2.1.2 反向傳播(Back Propagation) 8 2.1.3 卷積神經網路(CNN) 12 2.1.4 卷積神經網路之發展 17 2.2語意切割相關文獻 20 2.2.1 FCN 21 2.2.2 UNet 22 2.2.3 DeepLab系列 25 2.2.4 Mask R-CNN 29 2.3自注意力機制相關文獻 33 2.3.1 Vision Transformer 33 2.3.2 TransUNet 34 第三章 腦部腫瘤切割 36 3.1資料集介紹 37 3.2評估機制 38 3.3前處理 41 3.3.1 Z-Score 41 3.4資料擴增(Data Augmentation) 41 3.4.1 General Data Augmentation 41 3.4.2 Strong Data Augmentation 43 3.5模型架構 45 3.5.1 Overview 45 3.5.2 跳連結注意力機制 46 3.5.3 Transformer 49 3.5.4 深度監督 51 3.6模型訓練細節 54 3.7後處理 55 3.7.1 Small Connected Component 55 3.7.2 Small Enhancing Tumor 56 3.8推論推略 57 第四章 實驗結果 58 4.1消融實驗 58 4.2實驗結果可視化 63 4.3與他人技術比較 66 第五章 結論與未來展望 68 參考文獻 69

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