University of Guadalajara Workshop 2026

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Below is an annotated agenda for the 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; you may also want to go through the tutorials here. It is also recommended that you download version R2023a 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; instructions for downloading and installing SPM can be found here.

Day 1: Resting-State Fundamentals

Agenda

(9:00am-10:00am) Review of Matlab
This will be a brief review of Matlab and its fundamentals; these will be necessary for using the CONN toolbox, as well as more advanced methods such as scripting analyses. This lecture will cover:

  • Basics of navigation

  • Variables and Structures

  • Paths and Functions

  • Control Structures

  • Checking installation of SPM12; creating template job and loading it from the Matlab terminal.

(10:00am-12pm) Introduction to Functional Connectivity and the CONN Toolbox (Lecture & Practical)
This first practical will be a guided hands-on tutorial about how to open the CONN GUI and examine some of its features. We will review the following topics:

  • History of functional connectivity: Landmark studies, common issues with functional connectivity, uses and future potential

  • Functional vs. effective connectivity

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

  • The debate over Global Signal Regression, and other options you can change in your analysis

  • Overview of the CONN GUI

  • Creating a new project and loading the data

  • Initial quality checks

(12:00pm-1:00pm) Lunch Break

(1:00pm-2:00pm) Preprocessing the Individual Subject (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

  • Quality Assurance Checks: Alignment, outlier counts, and detection

(2:00pm-2:30pm) BIDS and Reproducible Analysis (Lecture by Lupita Yañez-Ramos)

  • Importance of standardized organization for data analysis

(2:45pm-4:00pm) 1st-Level Analysis and Group-Level Analysis (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

  • Examining the results for a single subject

  • Setting up group-level analyses in CONN

  • Second-level covariates and between-subject factors

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

  • Exporting data for use in other packages

(4:00pm-5:00pm) General Discussion, Q&A

Day 2: Functional Connectivity: Practice with the CONN Toolbox and Advanced Options

Agenda

(9:00am-9:45am) Review of Graph Theory (Lecture)

We begin the second half of our connectivity workshop with a brief overview of graph theory. Graph theory is closely related to the correlations between different brain regions. This lecture will cover the fundamentals you will need to understand the basic terms. In addition, we will apply this to the group-level results generated during the previous day, and learn how to interpret more advanced results.

  • Background of graph theory

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

  • Community detection

  • Correlation matrices and clinical applications

(9:45am-11:00am) Introduction to Task-Based Connectivity Analysis
The COON toolbox is also able to do task-based connectivity through a method known as PPI. We will demonstrate how to set up a generalized PPI (gPPI) analysis for a single subject. A custom atlas and covariate files can be found here.

  • Overview of PPIs

  • Importing timing files

  • Importing atlases

  • Running the analysis and interpreting the results

(9:45am-10:30pm) Setting up a General PsychoPhysiological Interaction (gPPI)
The COON toolbox is also able to do task-based connectivity through a method known as PPI. We will demonstrate how to set up a generalized PPI (gPPI) analysis for a single subject. A custom atlas and covariate files can be found here.

  • Overview of PPIs

  • Importing timing files

  • Importing atlases

  • Running the analysis and interpreting the results

(10:30am-12:00pm) Dynamic Connectivity and Surface-Based Connectivity
Dynamic connectivity measures temporal variability in functional connectivity. The most popular method is sliding-window analysis, which uses smaller intervals to measure connectivity changes over time. We will also learn about dyn-ICA, an independent components technique to identify networks that show similar temporal variations in functional connectivity.

  • Introduction to dynamic connectivity

  • Sliding-window analysis

  • How to set up a dyn-ICA analysis

  • Importing surface data output from FreeSurfer for surface-based analysis

  • Interpreting the results

(12:00pm-1:00pm) Lunch Break

(1:00pm) Group Photo

(1:00pm-1:30pm) Scripting your analysis
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. A template script can be downloaded here.

  • Creating your analysis script

  • Looping your analysis over subjects

  • How to obtain converted correlation-to-z values in a Matlab structure

(1:30pm-2:00pm) BIDS and Reproducible Analysis (Lecture by Lupita Yañez-Ramos)

  • Applied example of preprocessing anatomical and fMRI data

  • Demonstration of effective connectivity analysis in visual areas

(2:15pm-3:45pm) Analyzing a New Dataset (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.
As a group, we will select an open-access dataset to analyze (options will be provided by Andy). We will then determine how to analyze the dataset, and begin the processing of a single subject.

(4:00pm-5:00pm) General Discussion, Q&A