SPM for Basic and Clinical Investigators - Guangzhou

SPM8 for Basic and Clinical Investigators is an intermediate-level, 5-day workshop designed for investigators having familiarity with the fundamental principles of fMRI, with at least six months experience in functional neuroimaging data acquisition and analysis.

The workshop will focus on using SPM8 and its extensions for preprocessing, statistical modeling and visualization of data associated with a range of basic and clinical fMRI experimental designs. While the primary emphasis will involve using the core SPM8 programs for these purposes, there will also be extensive discussion of a variety of software tools that extend the power of SPM8. Some of these tools facilitate fMRI quality assurance through artifact detection and mitigation at various analysis stages. Other tools support a variety of data visualization methods, including MRIcron, xjView, FSLview and FreeSurfer.

As the presentations will include demonstrations and tutorials utilizing SPM8, participants are expected to bring a laptop with MATLAB, SPM8 and MRIcron already installed. Detailed setup instructions can be found here.

Each afternoon will end with an Analysis Workshop session, in which participants will gather in small groups to work through the stages of analyzing experiments using stuctural and functional neuroimaging endpoints.

The course website will provide guidance for subsequent self-study.

 

The course is co-organized by Center for the Study of Applied Psychology, South China Normal University and will be held at South China Normal University in Guangzhou, P.R. China from July 11-15, 2011.

Lectures will be held in the Instructional Center (RM 518-9) on the 5th floor of the SCNU School of Educational Science. about a 10 minute walk from the hotel.

The fee for the 5-day program is  US$1500. Reduced rates of US$1250 for post-doctoral fellows and US$1000 for undergraduate, graduate or medical students are available.  A 20% discount is available to all South China Normal University investigators.

 

Register for this program here.

You can arrange payment using PAYPAL here.

 

Accommodations for course participants are available at the Yuehai Hotel in Guangzhou. Course participants wishing to stay at the hotel can make reservations by contacting the hotel with their name, arrival and departure times.

GUANGZHOU YUEHAI HOTEL
39 Haiyuan Road,
510700 Guangzhou, China.
Telephone : 020－86006808

Questions about the course arrangements or content should be directed to support@neurometrika.org

The course instructors are Thomas Zeffiro and Susan Whitfield-Gabrieli.

 

The International Symposium on Brain Imaging: New Frontiers on Data Analysis 2011 will take place at South China Normal University the day before the course begins. Further details can be obtained by mailing Prof Li-Hai Tan at tanlh@hku.hk.

 

Educational Objectives 

  • Understand the basic organization of the SPM GUI
  • Understand the organization of the SPM "toolbox"
  • Be able to construct batch processing scripts for preprocessing and statistical modeling
  • Understand the basic fMRI data preprocessing steps
  • Be able to construct a preprocessing sequence including slice time correction, realignment, and spatial filtering
  • Understand the origins of the artifacts most commonly encountered in fMRI datasets
  • Be able to utilize explore an fMRI dataset for artifacts and effect repairs as needed
  • Understand the basic fMRI single subject experimental design types
  • Be able to implement statistical analysis procedures for the basic single subject fMRI designs
  • Understand the basic fMRI single group experimental design types
  • Be able to implement statistical analysis procedures for the basic single group fMRI designs
  • Understand the basic fMRI multiple group experimental design types
  • Be able to implement statistical analysis procedures for the basic multiple group fMRI designs
  • Understand the process of incorporation of covariates in fMRI experimental designs
  • Be able to construct and estimate statistical models involving covariates
  • Be able to utilize the RIC Talairach Daemon for region labeling
  • Be able to utilize the SPM Anatomy toolbox for region labeling
  • Be able to utilize the FreeSurfer for region labeling
  • Be able to export SPM statistical maps to FreeSurfer to visualize results on the cortical surface
  • Be able to use MRIcron for visualization, including volume rendering
  • Be able to use xjView for visualization and labeling
  • Understand the basic principles and procedures associated with ROI analysis

 

Schedule

Day 1

9:00AM-9:30PM  Course introduction

9:30AM-12:00PM  SPM introduction

  • SPM history
  • SPM architecture
  • The MATLAB environment
  • SPM toolboxes
  • SPM GUI
  • Batch editor
  • SPM Visualization

12:00PM-1:00PM LUNCH

1:00PM-4:30PM  Single subject analysis

  • Preprocessing
  • Model specification
  • Model estimation
  • Inference
  • Structure/function visualization

4:30-5:00 Homework assignment: Single subject analysis

Day 2

9:00AM-9:30PM  Homework review

9:30AM-12:00PM  Preprocessing

  • Preprocessing overview and background
  • Realignment
  • Unwarping
  • Slice time correction

12:00PM-1:00PM  LUNCH

1:00PM-3:30PM  Preprocessing

  • Spatial normalization
  • Spatial filtering
  • Introduction to EPI outlier detection and repair
  • Outlier detection using ART
  • ROI specification and processing

3:30PM-4:30PM  Statistics review: t-tests, regression, ANOVA, ANCOVA and the general linear model

4:30-5:00 Homework assignment: Preprocessing

Day 3

9:00AM-9:30PM  Homework review

9:30AM-12:00PM  First-level design

  • Experimental task design in fMRI
  • First-level design theory
  • First-level design demonstrations
  • Covariates in first-level designs

12:00PM-1:00PM LUNCH

1:00PM-4:30PM  First-level estimation and inference

  • First-level estimation
  • First-level design demonstrations
  • First-level contrast specification
  • First-level inference - critical thresholds

4:30PM-5:00PM  Homework assignment: First-level models 

Day 4

9:00AM-9:30PM  Homework review

9:30AM-12:00PM  Single group second-level design and estimation

  • Statistical modeling: summary statistics
  • Single group second-level design theory
  • Single group second-level design demonstration
  • Second-level contrast specification

12:00PM-1:00PM LUNCH 

1:00PM-4:30PM  Multiple group second-level design and estimation

  • Multiple group second-level design theory
  • Multiple group second-level design demonstration
  • Covariates in second-level design
  • Second-level design inference

4:30PM-5:00PM  Homework assignment: Second-level models

Day 5

9:00AM-9:30PM  Homework review

9:30PM-12:00PM  Artifact prevention, detection and mitigation

  • Sources of artifacts in EPI
  • Detection and repair of EPI artifacts
  • ART demonstration

12:00PM-1:00PM LUNCH 

1:30PM-3:30PM  Visualization, anatomical labeling and structural analysis

  • ROI analysis
  • Visualization with SPM8, FreeSurfer, MRIcron and xjview
  • Anatomical labeling with the Talairach Daemon, xjView and the SPM Anatomy Toolbox

3:30-4:30PM  Reporting an fMRI study

 

LECTURE SLIDES

SPM Overview

Optimizing fMRI Acquisition: Spatial

Optimizing fMRI Acquisition: Temporal

Preprocessing

Spatial Normalization

First Level Models

Second Level Models

Artifact Detection and Repair

ROI Processing

Reporting fMRI Results