Analysis of Functional Magnetic Resonance Imaging (Graduate)
Elective Course for the Graduate Students
Lecturer: Chia-Feng Lu
(alvin4016@ym.edu.tw)
功能性磁振影像分析 (醫放系研究所)
授課教師： 盧家鋒
學習目標 Learning Objectives
［全英文授課］修課學生將能了解功能性磁振造影基本成像與學習分析原理，包含造影條件、影像前處理、廣義線性模型、多體素模式分析、獨立成分網路分析、低頻強度分析、功能性連結分析、與圖學分析。透過原理講授、隨堂實作與相關文獻討論，修課學生將能掌握實作分析能力，協助自身研究發展。
Students should be able to learn the principles and analyses of functional magnetic resonance imaging (fMRI), including the imaging parameters, standard preprocessing, general linear model, multi-voxel pattern analysis, independent component analysis, amplitude of low-frequency fluctuation, functional connectivity, and graph theory. Through the given lectures, hands-on practices, and literature review, students should be able to handle the essential analysis skills to facilitate their own researches in the fMRI field.
先備能力之需求 Required Previous Knowledge
磁振影像學、神經解剖學與程式語言。
Basic knowledge of magnetic resonance imaging, neuroanatomy and MATLAB programming skills.
上課地點Classroom
一教131室
授課內容 Syllabus
Week 1： Course Introduction and Overview
＜Handout＞Lesson1_slides.pdf
＜Videos＞please watch in 720p video resolution
(1) Course Overview (1:11:47)
Week 2： Principles of BOLD fMRI
＜Handout＞Lesson2_slides.pdf
＜Videos＞please watch in 720p video resolution
(1) Physiology of Neural Activity (47:42)
(2) Principles of fMRI (45:20)
Week 3： Experimental Design of BOLD fMRI
＜Handout＞Lesson3_slides.pdf
＜Videos＞please watch in 720p video resolution
(1) Experimental Design - Part 1 (35:00)
(2) Experimental Design - Part 2 (40:55)
Week 4： Neuroanatomy and Image Atlas
＜Handout＞Lesson4_slides.pdf
＜Materials＞ImageAtlasUI.zip
＜Videos＞please watch in 720p video resolution
(1) Neuroanatomy of Cerebral Cortex (53:14)
(2) White Matter and Image Atlas (26:37)
Week 5： Visit of YM 3T-MRI Facility - Data Acquisition
＜Handout＞Lesson5_slides.pdf
＜Videos＞please watch in 720p video resolution
Week 6： Image Preprocessing of fMRI
＜Handout＞Lesson6_slides.pdf
＜Materials＞fMRIana06_materials.zip (updated)
＜Videos＞please watch in 720p video resolution
(1) DICOM Format and Conversion (35:20)
(2) Image Preprocessing Using SPM Batch (48:40)
Week 7： Brain Activation - General Linear Model: Part I
＜Handout＞Lesson7_slides.pdf
＜Materials＞fMRIana07_materials.zip
＜Videos＞please watch in 720p video resolution
(1)Setup of SPM Preprocessing Batch (50:47)
(2)General Linear Model (45:32)
Week 8： Brain Activation - General Linear Model: Part II
＜Handout＞Lesson8_slides.pdf
＜Materials＞fMRIana08_materials.zip
＜Videos＞please watch in 720p video resolution
(1)SPM 1st-level Analysis (32:38)
(2)SPM 2nd-level Analysis (40:52)
Week 9： Resting-State Brain Activity - ReHo and ALFF
＜Handout＞Lesson9_slides.pdf
＜Materials＞fMRIana09_materials.zip
＜Videos＞please watch in 720p video resolution
(1)Resting-state fMRI Analysis (41:47)
(2)DPABI toolbox (30:36)
Week 10： Brain Network - Independent Component Analysis
＜Handout＞Lesson10_slides.pdf
＜Materials＞fMRIana10_materials.zip
＜Videos＞please watch in 720p video resolution
(1) Independent Component Analysis of fMRI (36:29)
(2) GIFT toolbox (56:20)
Week 11： Brain Network - Functional Connectivity
＜Handout＞Lesson11_slides.pdf
＜Materials＞fMRIana11_materials.zip
＜Videos＞please watch in 720p video resolution
(1) Functional Connectivity of fMRI (32:18)
(2) DPABI toolbox - Functional Connectivity (39:48)
Week 12： Brain Network - Dynamic Casual Modeling
＜Handout＞Lesson12_slides.pdf
＜Materials＞fMRIana12_materials.zip
＜Videos＞please watch in 720p video resolution
(1) Dynamic Causal Modeling of fMRI (33:19)
(2) DCM analysis using SPM12 (55:31)
Week 13： Brain Network - Dynamic Functional Connectivity
＜Handout＞Lesson13_slides.pdf
＜Materials＞fMRIana13_materials.zip
＜Videos＞please watch in 720p video resolution
Week 14： Brain Network - Graph Theory and Topological Properties
＜Handout＞Lesson14_slides.pdf
＜Materials＞fMRIana14_materials.zip
＜Videos＞please watch in 720p video resolution
(1) Brain Network - Graph Theory (37:14)
(2) GRETNA and BrainNet Toolbox (55:58)
Week 15： Brain Decoding - Multivariate Pattern Analysis: Part I
＜Handout＞Lesson15_slides.pdf
＜Materials＞fMRIana15_materials.zip
＜Videos＞please watch in 720p video resolution
(1) Brain Decoding - MVPA (48:17)
(2) PRoNTo Toolbox for MVPA (47:45)
Week 16： Brain Decoding - Multivariate Pattern Analysis: Part II
＜Handout＞Lesson16_slides.pdf
＜Videos＞please watch in 720p video resolution
Week 17： Final Report: Part I
Week 18： Final Report: Part II
課程參考資料 References
- William D. PennyKarl J. FristonJohn T. AshburnerStefan J. KiebelThomas E. Nichols, Statistical Parametric Mapping: The Analysis of Functional Brain Images, Elsevier, 2011.
- Alex FornitoAndrew ZaleskyEdward Bullmore, Fundamentals of Brain Network Analysis, Academic Press, 2016.
- Stephan UlmerOlav Jansen, fMRI: Basics and Clinical Applications, 2nd Edition, Springer Science & Business Media, 2013.