Learning the CONN Toolbox

Using the CONN Toolbox for Functional Connectivity Analysis

Susan Whitfield-Gabrieli, Ph.D., Program Director 
Robert L. Savoy, Ph.D., Program Administrator ( send all questions regarding this program to savoy@nmr.mgh.harvard.edu )


The next edition of this program will be held during the week of April 27 - May 1, 2020 (Monday - Friday).

General information, registration, payment, and accommodation information is shown below.  If you have specific questions, please contact us here.  

The Program

Faculty (in brief)
Registration and Fees
Payment Methods (After Registration)
Minimum and Maximum Number of Participants
Venue for the workshop
Reserving Accommodations
Preparing your laptop



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 reveals 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 first and most widely used technique for analyzing such data has been correlation based analysis of the connections between seed regions in the brain. Today there are a host of additional methods to analyze the data. A premier software package that implements this array of techniques is the CONN toolbox, created by Susan Whitfield-Gabrieli and Alfonso Nieto Castañòn.

    CONN is an toolbox for functional connectivity analyses in the resting state and during task. It is ranked among the top-10 most visited and downloaded neuroimaging tools and resources at NITRC, with over 40,000 downloads and a very active user community, and it has been cited and used in over 400 papers (the 2nd most cited reference in the Brain Connectivity journal).  While it was developed in the context of SPM and Matlab, it is now available in standalone forms as well.  The last versions can normally be found at the NITRC site and pushing the “See All Files” button.

    The present program will consist of five 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.

    Please note:  (1) Registration is limited     (2) Exercises will be conducted on participant laptops     (3) There will be homework!



The faculty for this program includes the originators and developers of the CONN Toolbox, and several expert users and teachers to help with the interactive portion of the program. The list is:

Susan Whitfield-Gabrieli Organizer and keynote speaker at this program. At the 2015 meeting of the Organization for Human Brain Mapping, she gave a keynote address on the topic of Connectomic Insights into Psychiatric Disorders. She is now the Director of the NUBIC: Northeastern University Biomedical Imaging Center, and Professor of Psychology at Northeastern University in Boston. See  https://cos.northeastern.edu/people/susan-whitfield-gabrieli/
 Alfonso Nieto Castañòn Principle lecturer at this program, and the primary software developer of CONN. He is also an active computational neuroscientist researcher. See http://www.alfnie.com/home
 Sheeba Arnold Anteraper Lecturer and primary resource for hands-on assistance to participants learning CONN during the program.  She is a Principle Research Scientist at the NUBIC. Click on her link at: https://web.northeastern.edu/nubic/about/team/
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. See https://www.martinos.org/investigator/robert-savoy/







Registration and Fees    To Register, click http://education.martinos.org/educational-courses/using-the-conn-toolbox-for-functional-connectivity-analysis/ 

Enrollment is limited to 46 people. Early registration is recommended. 

Fee Schedule is as follows:
        Regular:    $1500
        Post-Doc:  $1250
        Student:    $1000


Paying Registration Fee (after registering) To make a payment, click here.   

The preferred method of payment is via credit card.  

      NOTES about payment via credit card:  

                The secure payment is handled by PayPal, but there is an option to pay via credit card, as usual.

                Successful transactions end with a receipt page you can print; and if you include your e-mail address on the final payment screen with credit card information, PayPal will also send you an e-mail copy of the receipt.

To arrange payment via an electronic funds transfer (EFT) please contact us directly, as shown near the beginning of this page.


Minimum and Maximum Number of Participants

Maximum enrollment is normally limited to 46 people.  On occasion we have expanded that to 53.

The minimum number of registered participants required to hold the program is 20. (It is very unlikely that the program will not be held because of not reaching the minimum enrollment.) 



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.


DAY 1 

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



The conference will be held at The Martinos Center for Biomedical Imaging, whose street address is: 149 Thirteenth Street, Charlestown, MA  02129  USA


Accommodations will be at a special rate at the     The Constitution Inn across the street from the classroom.  Please mention MGH and "Learning the CONN Toolbox" when making a reservation there.



Preparing your laptop computer for the program

The best way to run CONN is by having a MATLAB license (from Mathworks) and running that version.  But the standalone versions that do not require a MATLAB license are fully adequate for the purposes of this workshop.  Both are available at the NITRC site by pushing the “See All Files” button and selecting the appropriate option.  There will also be storage requirments on your laptop of approximately 30 Gig for all the exercises.