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fMRI: Back to Basics
Weekend Course
ORGANIZERS: Benedikt Poser, Susan Francis, Richard Buxton, Xin Yu
Saturday, 11 May 2019
| Room 512A-H |
08:00 - 11:25 |
Moderators: Susan Francis, Sriranga Kashyap |
Skill Level: Basic
Session Number: WE-04
Overview
This session will cover introductory and intermediate topics in BOLD fMRI acquisition and analysis, including basic task based and resting state fMRI analysis using general linear model and data-driven analysis approaches, respectively, as well as a couple of topics in advanced functional MRI and high spatial and temporal resolution.
Target Audience
This course is designed for basic and clinical researchers who would like to get a broad, basic-level introduction to fMRI, from acquisition to analysis.
Educational Objectives
As a result of attending this course, participants should be able to:
- Describe basic BOLD signal physiology;
- Recall aspects related to fMRI acquisition and preprocessing;
- Explain the considerations behind the design of task fMRI experiments;
- Describe the analysis approach to task and resting-state fMRI; and
- Identify opportunities and pitfalls of fMRI at high spatial and/or temporal resolution.
08:00
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Basic BOLD Physiology
Avery Berman
Functional MRI (fMRI) based on the blood oxygenation level-dependent (BOLD) signal has been used by researchers over the last 25+ years to non-invasively map brain activity and to measure brain physiology. This lecture will explain the basic biophysical principles that enable the use of the BOLD signal as a surrogate measure of brain activity. Topics covered fall into the domains of BOLD-related cerebrovascular physiology (basics of neurovascular coupling) and BOLD MR physics (blood oxygenation-dependence of T2 and T2*). Building on this basic understanding will help us better interpret BOLD signals and their spatial specificity.
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08:25
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Data Acquisition Basics
Saskia Bollmann
This course gives an introduction to data acquisition for fMRI using echo planar imaging (EPI). Key sequence parameters (voxel size, repetition time, echo time, echo train length, flip angle, parallel imaging, simultaneous multislice) and typical artifacts (ghosting, distortions, signal loss) and their impact on contrast, geometry and speed of EPI time series will be discussed.
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08:50
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Preprocessing
Cesar Caballero-Gaudes
This talk will describe the main steps of functional MRI data preprocessing based on the blood-oxygenation level dependent (BOLD) contrast. The numerous methods available for each step, and corresponding parameter selection, causes that the amount of possible preprocessing workflows can be enormous, which may lead to substantial variability in the quality of the preprocessed data and final results. We will establish some simple guidelines for adequate preprocessing since there is no ‘optimal’ preprocessing pipeline, but there are incorrectly applied methods, emphasizing that the workflow must be decided according to the characteristics of each dataset and the research question. We will briefly introduce several platforms that can help researchers to design the preprocessing pipeline, automatize its execution, and facilitate data quality assessment. These tools can foster reproducibility, and ensure transparent reporting of methodological details.
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09:15
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Task-Based fMRI
Alessio Fracasso
Task-based fMRI data is often analysed using the General Linear Model (GLM). This talk introduces this analytical approach starting from its basic concepts, benefits and limitations. Examples will be given showing how it can be used in block and event-related paradigms. Furthermore, the discussion will cover an introduction to the flexible use of the GLM in forward (or encoding) modelling approaches of task-based fMRI as the population receptive field (pRF) analysis.
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09:40
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Break & Meet the Teachers |
10:10
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Resting-State fMRI
Ann Choe
In this educational course, basic concepts of the resting state fMRI (rsfMRI) will be outlined, and several widely used data-driven analysis approaches for resting state functional connectivity (rsFC) and their applications will be introduced. The course will also briefly describe the recent emergence of dynamic functional connectivity (dFC) and several of its widely used data analysis approaches.
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10:35
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High Spatial Resolution fMRI
Jeroen Siero
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11:00
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High Temporal Resolution fMRI
Laura Lewis
Whole-brain fMRI data can now be acquired at high temporal resolution – on timescales of hundreds of milliseconds. These ‘fast fMRI’ approaches have the potential to reveal new information about brain function. Both acquisition and analysis techniques need to be adapted for fast fMRI in order to exploit its full potential for neuroscience. This lecture will provide an overview of techniques for fast fMRI, how to design fast fMRI studies, and how to model and analyze fast fMRI data. Finally, we will discuss the advantages and limitations of fast fMRI, and highlight potential confounds in interpreting fast fMRI data.
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11:25
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Lunch & Meet the Teachers |
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