Learning the CONN Toolbox for Functional Connectivity Analysis

April 27 – May 1, 2020

Resting-state functional connectivity has taken the brain imaging community by storm. Five to ten minutes of MRI data collection from almost any subject or patient can reveal organized systems of activity in the brain that can be used in a wide variety of ways for basic and clinical research, and even to guide non-invasive brain stimulation. The primary tool for analyzing such data has been correlation-based analysis of the connections between seed regions in the brain. A premier software package for such analysis is the CONN toolbox, created by Susan Whitfield-Gabrieli and Alfonso Nieto Castañòn.

CONN is an SPM-based toolbox for functional connectivity analyses in the resting state and during tasks. It is ranked as one of the top 10 most visited and downloaded neuroimaging tools and resources at NITRC, with over 40,000 downloads and a very active user community. Also, it has been cited and used in over 400 papers (the second-most cited reference in the Brain Connectivity journal).

The program consists of three intensive days of training in the use of this software. Participants will bring their own laptop computers; classroom presentations will be followed by substantial time using the packages with expert guidance available.


The faculty for the program includes the originators and developers of the CONN Toolbox and several expert users and teachers to help with the interactive portion of the training:

Susan Whitfield-Gabrieli: Software developer and principal speaker at this program. She was a keynote speaker at the 2015 meeting of the Organization for Human Brain Mapping, speaking on the topic of Connectomic Insights into Psychiatric Disorders.
Alfonso Nieto Castañòn: A prize-winning Matlab Programmer; software developer of CONN; an active computational neuroscientist researcher.
Sheeba Arnold Anteraper: Senior Programmer at the McGovern Institute, and an expert user of CONN.
Robert L. Savoy: Organizer of numerous brief, intense training programs at the Martinos Center for Biomedical Imaging of the Massachusetts General Hospital and elsewhere around the world.




Sample Schedule

The details and exact order of the schedule below are likely to be modified as the program approaches.   Information from registrants about adding specific topics will be strongly considered and accommodated if possible.

 The “Final Application Lecture” may be re-scheduled to a time earlier in the week; perhaps the end of one of the days (probably Wednesday), or after a group dinner on that evening.



Morning Program Introduction Susan Whitfield-Gabrieli
Approaches to MultiVariate Analysis and Functional Connectivity Robert Savoy
MATLAB and its Relationship to The CONN Toolbox faculty
Orientation to Relevant Software Packages Susan Whitfield-Gabrieli
 Afternoon Resting State Connectivity: History; Examples; Cautionary Stories Susan Whitfield-Gabrieli
Orientation to the Specifics of the CONN Toolbox     faculty
Preprocessing: Artifact Prevention, Detection, and Mitigation Susan Whitfield-Gabrieli
Homework Assignment: Preprocessing


Morning Homework Review: Preprocessing
Single Subject Processing in CONN Susan Whitfield-Gabrieli
Homework Assignment: Single Subject Processing
Afternoon Single Group Second-Level Design Susan Whitfield-Gabrieli
Single Group Second-Level Estimation Susan Whitfield-Gabrieli
Homework Assignment: Single Group


Morning Homework Review: First Level Analysis
Multiple Group Second-Level Design Alfonso Nieto Castañón
Multiple Group Second-Level Estimation Alfonso Nieto Castañón
Homework: Second Level (NYU Group Data)
Afternoon Review/Discussion of Basic CONN Toolbox faculty
Overview of Advanced Features in the CONN Toolbox: Alfonso Nieto Castañón
     ROI-to-ROI Analyses
     Graph Theory
     Voxel-to-Voxel Analyses
     Surface-Based Analysis
     Dynamic Connectivity
     Latest CONN Features:


Morning Homework Review: Second Level Analysis
Connectome Analysis: ROI-to-ROI Alfonso Nieto Castañón
Connectome Analysis: Graph Theory Alfonso Nieto Castañón
Homework: ROI-to-ROI & Graph Theory
Afternoon Connectome Analysis: Voxel-to-Voxel Alfonso Nieto Castañón
Connectome Analysis: Surface-Based Alfonso Nieto Castañón
Homework: Voxel-to-Voxel & Surface-Based


Morning Homework Review: Voxel-to-Voxel & Surface
Connectome Analysis: PPI Alfonso Nieto Castañón
Connectome Analysis: Dynamic Connectivity Alfonso Nieto Castañón
Connectome Analysis: Latest Features Alfonso Nieto Castañón
Homework-during-Lunch! PPI & Dynamic Connectivity
Afternoon Homework Review: PPI & Dynamic Connectivity
Final Application Lecture (may be scheduled earlier in week) Susan Whitfield-Gabrieli
Informal Discussion faculty