Network Analysis: Functional Connectivity - Baltimore

Network Analysis is an advanced, 5-day workshop designed for investigators having familiarity with the basic principles of fMRI data acquisition, statistical analysis using the general linear model, and substantial practical experience using SPM.

The presentations will provide an introduction to network analysis using SPM8, FSL and AFNI along with practical demonstrations tied to the key conceptual issues. The focus will be on techniques other than the usual massively univariate analyses commonly used for modeling fMRI data. Topics covered will include functional connectivity examined using bivariate correlation or regression, independent components analysis and graph theory.

Participant Preparation: The workshop will involve demonstrations and interactive exercises involving SPM8, its extensions and associated programs. These demonstrations will be integrated with the didactic portions of the lectures.

The interactive software exercises will demonstrate the details of the various data modeling techniques and participants will gain practical experience through the worked examples. Therefore, to gain the full benefit from the program, we ask that participants bring laptops with MATLAB and SPM8 installed. Detailed setup instructions can be found here.

This course will be sponsored by the Johns Hopkins Brain Science Institute. It will be held from DEC 12-16, 2011 in the School of Nursing Building (515 N. Wolfe Street, Baltimore, MD 21205), located on the Johns Hopkins East Baltimore campus.

Directions to the classrooms in the School of Nursing Building can be found here. Lectures will be held in Room 305 on Monday, Room 217 on Tuesday and Wednesday, Room 202 on Thursday and Room 217 on Friday.

Lodging near the medical campus is available at McElderry House.

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

This course will be taught by Tom Zeffiro and Susan Whitfield-Gabrieli.

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

Tentative Schedule

Day 1

Background to network analysis

9:00AM-12:00PM

Introduction and software installation
SPM overview and demonstration
fMRI analysis overivew: modeling, estimation and inference
Single subject analysis demonstration

12:00PM-1:00PM Lunch

1:00PM-4:30PM

Network analysis overview
Optimal fMRI data acquisition
Preprocessing
First level design and analysis
Design workshop introduction
Homework assignment - Single subject block design analysis

pdf of references

Day 2

Functional connectivity analysis

9:00AM-12:00PM

Review of single subject block design analysis
ROI processing overview
Creating anatomical and functional masks
ROI data extraction using REX
REX demonstration
Functional connectivity analysis demonstration

12:00PM-1:00PM Lunch

1:00PM-4:00PM

Artifact detection and mitigation using ART
ART demonstration
Introduction to the Connectivity Toolbox
- functional connectivity analysis demonstrations

The functional connectivity toolbox manual can be found here.

Connectivity Toolbox dataflow chart

Here is a single-subject analysis exercise.

4:00-5:30 Design workshop

Day 3

Functional connectivity analysis

9:00AM-12:00PM

Review of single-subject functional connectivity analysis homework
Connectivty Toolbox processing steps
- Setup
- Preprocessing
- First level analysis
Single subject demonstration

12:00PM-1:00PM Lunch

1:00PM-4:00PM

Using the Connectivity Toolbox for group analysis
- Group analysis demonstration
Connectivity Toolbox group analysis practice session
Homework assignment group analysis (NYU data set)

4:00PM-5:30PM Design workshop

Here are some example connectivity toolbox batch files:

complete batch file - setup - preprocessing - analyses - results

Day 4

Graph Theory

9:00AM-12:00PM

Review of group functional connectivity analysis homework
Specifying covariates in the Connectivity Toolbox
Graph theory
- The single-subject graph theory demonstration instructions can be found here.
- The resting state multi-subject graph theory demonstration instructions can be found here.

12:00PM-1:00PM Lunch

1:00PM-4:00PM