Learning the CONN Toolbox
Using the CONN Toolbox for
Seed-Based Functional Connectivity Analysis
Susan Whitfield-Gabrieli, Ph.D., Program Director
Robert L. Savoy, Ph.D., Program Administrator ( send all questions regarding this program to firstname.lastname@example.org )
The next edition of this program will be held during the week of May 1-5, 2017 (Monday - Friday) at the Martinos Center.
General information, registration, payment, and accommodation information is shown below. If you have specific questions, please contact us here.
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 primary tool for analyzing such data has been correlation based analysis of the connections between seed regions in the brain; and 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 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).
The present program will consist 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.
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 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.
For more information about the faculty for this program, click here.
Registration and Fees To Register, click here.
Enrollment is limited to 46 people. Early registration is recommended.
Fee Schedule is as follows:
Paying Registration Fee (after registering) To make a payment, click right here.
The preferred method of payment is via credit card, by clicking above.
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 pay by check, click here.
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 limited to 46 people.
The minimum number of registered participants required to hold the program is 20. (The program held during the summer of 2015 in Cincinnati filled at 30 people; we have a larger room available here. 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.
|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||
|Homework Assignment: Single Subject Processing|
|Afternoon||Single Group Second-Level Design||
|Single Group Second-Level Estimation||
|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|
|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|
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 primary requirement for your computer is that it can run MATLAB (from Mathworks). There will also be storage requirments on your laptop, of approximately 30 Gig for all the exercises.