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
2. Install the CONN Toolbox
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,
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 humanconnectome.org or openneuro.org.
(3:00pm-4:00pm) General Q&A
Please fill out the feedback form here at the end of the workshop!