Brain Connectivity Methods - Philadelphia

Brain Connectivity Methods is a highly interactive and intensive workshop designed for investigators having familiarity with the basic principles of fMRI data acquisition, statistical analysis using the general linear model, and some practical experience using SPM for fMRI analysis.It will be held MAR 7-10, 2017 at Temple University in Philadelphia, PA and will include subsequent online interactive sessions.

The course will feature presentations from experts in the use of SPM12, CONN: The Connectivity Toolbox and the HCP Connectome Workbench. It will provide an introduction to functional brain connectivity analysis using these programs along with practical demonstrations and exercises tied to the key conceptual issues. Topics covered will include functional brain connectivity examined using bivariate correlation or regression, independent component analysis, and graph theory. The principal focus of the course is mastery of the essential skills needed for using functional connectivity analysis techniques to analyze resting state fMRI data.

Other workshop highlights include:
Process automation using batch processing in SPM12/CONN and the Connectome Workbench
fMRI data acquisition optimization
Special considerations when collecting multiband EPI data
Geometric distortion correction
Physiological denoising techniques
-Control of physiological/movement confounds using CompCor
-Artifact detection and elimination using the ART Toolbox

Participant Preparation: The workshop will involve demonstrations and interactive exercises involving SPM12/CONN Toolbox and the HCP Connectome Workbench, their 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. Participants will gain practical experience through the worked examples based on resting state data provided at the course. Therefore, to gain the full benefit from the program, we ask that participants bring laptops with SPM12/CONN and the Connectome Workbench installed. Detailed setup instructions can be found here.

temple-university
As mastery of the topics presented early in the week is needed to maximally benefit from the material presented later in the week, we encourage all participants to arrange their schedules to make it possible to attend all the classes.

Approximately one month after the course we will arrange on-line review sessions so that participants will be able to ask questions that may arise as they gain experience with the software.

To allow a high degree of student-faculty interaction, the class will be limited to 25 participants. Subsequent interactive on-line sessions held after the class will allow students to continue developing proficiency in connectivity analysis. 

Registration information for this program may be found here

Payment of the registration fee ($1500-regular, $1250-fellow, and $1000-student) may be made with PAYPAL here.

The course will be held  March 7-10, 2018  at Temple University in Wachman Hall Room 108.

Accommodations: There are rooms available on campus at the Conwell Inn.

Questions about the course content should be directed to spmbasics@neurometrika.org 

Lectures will be given by Tom Zeffiro, with guest lectures by other instructors.

Educational Objectives 

  • Understand the basic organization of the SPM GUI
  • Understand the organization of the CONN Toolbox
  • Understand the organization of the HCP Connectome Workbench
  • 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 resting state experimental design types
  • Be able to implement statistical analysis procedures for the basic single subject fMRI rsting state designs
  • Understand the basic single group design types
  • Be able to implement statistical analysis procedures for the basic single group designs
  • Understand the basic multiple group design types
  • Be able to implement statistical analysis procedures for the basic multiple group designs
  • Understand the process of incorporation of covariates in experimental designs
  • Be able to construct and estimate statistical models involving covariates
  • Be able to utilize the SPM Anatomy toolbox for region labeling
  • Be able to use MRIcron for visualization, including volume rendering
  • Be able to use xjView for visualization and labeling
  • Understand the basics of graph theory

 

Tentative Schedule

Day 1

 Background to network analysis

10:00AM-12:00PM

  • Introduction
  • SPM12 overview
  • fMRI analysis overview: modeling, estimation and inference
  • Preprocessing review
  • Single subject analysis demonstration 

12:00PM-1:00PM Lunch

1:00PM-2PM

Introduction to the CONN Toolbox

2:00PM-3:00PM

Introduction to the HCP Connectome Workbench

3:00PM-5:00PM

Network analysis overview: Part I

  • Group models: Repeated measures and contrasts

Homework: SPM analysis of auditory data

pdf of references

Day 2

Functional connectivity analysis

9:00AM-10:00PM

  • Homework review: SPM auditory example

10:00AM-11:00AM

  • Functional connectivity overview: Part 2

11:00PM-12:00PM

  • CONN Toolbox processing steps
    • Setup
    • Preprocessing
    • First level analysis

12:00AM-1:00PM Lunch

1:00PM-2:00 PM

Connectome Workbench processing steps

  • Setup
  • Preprocessing
  • First level analysis

2:00-4:00PM

  • Quality assurance in functional connectivity analysis
  • Outlier detection and mitigation using ART
  • ART demonstration

The functional connectivity toolbox manual can be found here.

CONN Toolbox dataflow chart

Homework:

  • Here is a single-subject analysis exercise.
  • Homework assignment group analysis (NYU data set)

 

Day 3

Functional connectivity analysis

9:00AM-10:00PM

  • Homework Review: Single-subject functional connectivity analysis homework

10:00AM-12:00PM

  • Using the CONN Toolbox for group analysis
  • Group analysis demonstration
  • CONN Toolbox group analysis practice session

12:00PM-1:00PM Lunch

1:00PM-3:00PM

  • Using the Connectome Workbench for group analysis
  • Group analysis demonstration
  • Connectome Workbench group analysis practice session

3:00PM-4:00PM

  • Specifying and interpreting covariates
  • 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.

Here are some example connectivity toolbox batch files:

complete batch file - setup - preprocessing - analyses - results

 

Day 4

Functional connectivity analysis

9:00AM-10:00PM

  • Homework review: group connectivity analysis

10:00AM-12:00PM

  • Second level models

12:00PM-1:00PM Lunch

1:00PM-3:00PM

  • Optimal fMRI Data Acquisition

3:00PM-4:00PM

  • ROI analysis

Homework: TBD

LECTURE SLIDES

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