CONN Toolbox Workshop 2018

Welcome to the Amherst CONN toolbox workshop! To prepare for the course, do the following steps:

1. Get Started with Matlab

Please watch this playlist for an introduction to Matlab and its basic commands. It is also recommended that you download version R2017a or later.

2. Install the CONN Toolbox

Use this link for instructions on how to download and install the CONN Toolbox. Note that CONN also requires the SPM package, which can be downloaded here.

3. Download the Dataset

The dataset we will use for this workshop is from the NYU test-retest experiment, which can be found here.

Day 1: Introduction to Functional Connectivity, Graph Theory, and the CONN Toolbox



(10:00am-11:00am) Review of Functional Connectivity (Lecture)
This will be a brief overview of functional connectivity and how it relates to fMRI data.

  • Functional vs. effective connectivity

  • Basics of functional connectivity: Scrubbing, ROIs, correlations between regions

  • Resting-state specific preprocessing

  • The debate over Global Signal Regression

(11:00am-12:00pm) Overview of Graph Theory
Graph theory is closely related to the correlations between different brain regions. This second lecture will cover the fundamentals you will need to understand the basic terms.

  • Background of graph theory

  • Basics of graph theory: Nodes, edges, modularity,

  • Community detection

  • Correlation matrices and clinical applications

(1:00pm-2:15pm) Preprocessing the Individual Subject (Lecture & Practical)
This practical will show how to preprocess the data for a single subject in CONN.

  • Realignment, slice-timing, and outlier detection

  • Loading the SPM.mat file

  • Data denoising and detrending

  • Checking normalization and smoothing

(2:15pm-3:00pm) Quality Assurance (Practical)
As with all neuroimaging data, quality assurance checks are very important. After reviewing some common examples of quality failures, you will examine your own data.

  • Checking registration between T1 and T2 modalities

  • Alignment of the outline of the brain vs. alignment of internal structures

  • Outlier counts and detection

(3:00pm-4:00pm) General Q&A*
This is an opportunity to ask questions about any of the topics covered during the day.

*Any issues with Matlab or the CONN Toolbox will be addressed during this session.

Day 2: Practice with the CONN Toolbox and Advanced Options



(10:00am-11:15am) Group-level analysis (Lecture & Practical)
An overview of how to set up group-level analyses, as well as caveats to be aware of.

  • Setting up group-level analyses in CONN

  • Second-level covariates and between-subject factors

  • Correction mechanisms: FWE, FDR, and cluster-forming thresholds

(11:15am-12:00pm) Viewing the Results (Practical)
We will tour CONN’s visualization tools, and learn how to interpret the results.

  • Thresholding your connectivity maps

  • Rendering connectivity maps onto surfaces

  • Viewing node connectivity maps

(1:00pm-1:45pm) Scripting your analysis (Practical)
Automating analyses is an indispensable skill for the neuroimaging researcher. This practical will demonstrate how to script analyses in the CONN toolbox, which can speed up processing and reduce the likelihood of error.

  • Creating your analysis script

  • Looping your analysis over subjects

(1:45pm-3:00pm) Working with your own data (Practical)
The concepts and tools we have discussed so far should provide you with enough knowledge to begin to analyze your own data. This session will be devoted to beginning your own analysis with CONN. This can either be your own data, or a dataset downloaded from an online repository, such as or

(3:00pm-4:00pm) General Q&A

Please fill out the feedback form here at the end of the workshop!