臺灣博碩士論文加值系統

醫學影像分析中，大腦皮質下的分割是其中一項重要的任務。許多神經、神經衰退疾病與皮質下的區域相關，像是阿茲海默症、自閉症、亨丁頓舞蹈症等，要是能快速並準確的分割，能夠在早期幫助專家進行診斷或評估。經由專家的手動分割被認為是一種標準，但是通常相當費工與耗時，難以應用在較大的資料集上，因此顯現了自動化皮質下分割的重要性。在這篇論文中，我們利用7039筆3D T1w MRI的搭配FreeSurfer產出的分割結果作為輔助標籤訓練3D U-Net網路，經由四個實驗對模型進行最佳化，透過不同面向去評估模型選出最好的模型，並嘗試將模型應用在臨床的研究上，經由預測ADNI資料集的大腦體積進一步分析阿茲海默症患者與正常受試者的海馬迴體積衰減差異，觀察分割結果與實際病理狀況是否相符合。最終，透過多面向的實驗得出了一個快速、穩定、準確度高的模型，其分割結果與手動分割的體積誤差較低，並且實際應用在病理影像上能成功觀察出相對應的趨勢，在臨床的研究上將有利於專家進行快速的分析。

Subcortical brain segmentation is considered an important task in neuroimaging analysis. Many neurological and neurodegenerative diseases are related to subcortical areas, such as Alzheimer's disease, Autistic spectrum disorder, Huntington’s disease, etc. If the subcortical region can be segmented quickly and accurately, it will help experts diagnose or assess the condition early. Manual segmentation by experts is considered the gold standard. Still, it is often labor-intensive, time-consuming, and difficult to apply to larger datasets, thus highlighting the importance of automated subcortical segmentation. In this study, we used 7039 3D T1-weighted MRIs with FreeSurfer's segmentation results as auxiliary labels to train 3D U-Net, optimized the model through four experiments, evaluated the model through different aspects to select the best model, and tried to apply the model to clinical research. By predicting the brain volume of the ADNI dataset, we further analyzed the difference in the volume attenuation of the hippocampus between Alzheimer's patients and normal subjects and observed whether the segmentation results were consistent with the actual pathological conditions. Finally, a fast, stable, and high-accuracy model were obtained through multi-faceted experiments. The volume error of the segmentation results and manual segmentation was lower than FreeSurfer. The actual application of the model can successfully observe the corresponding trend in pathological images, which can be helpful for experts to conduct rapid analysis in clinical research.

Table of contents
Abstract i
中文摘要 ii
List of Figure iv
List of Table v
Chapter 1: Introduction 1
Chapter 2: Materials and Methods 4
2.1 Dataset 4
2.1.1 Training dataset 4
2.1.2 Testing dataset 6
2.1.3 Scan-rescan dataset 7
2.1.4 ADNI dataset 9
2.2 Data preprocessing 10
2.3 Model training 11
2.4 Evaluation 11
Chapter 3: Model Optimization 13
3.1 Exp-1: Different resolution of input data 13
3.2 Exp-2: Training model in high resolution 16
Chapter 4: Model Evaluation 19
4.1 Exp-3: The estimation of subcortical volume 19
4.2 Exp-4: Reproducibility of model 21
Chapter 5: Hippocampal volume loss in Alzheimer’s disease 24
Chapter 6: Discussion and conclusion 30
Reference 35

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