Course curriculum

  • 1

    Getting Started

    • Welcome!

    • Schedule for the Program

    • Computer Setup and Data Download and Processing

    • Participant Biosketches
  • 2

    Confidentiality Agreement for Program Material and Sessions

    • Participation Agreement 2024

    • Participation Agreement Attestation
  • 3

    Shared Question Page INFORMATION

    • Shared question page (To be set up for this program)
  • 4

    References and Suggested PreCourse Readings

    • Precourse Readings and References

    • Handbook of Functional MRI Methods in CONN by Alfonso Nieto-Castañón

    • Mid Course Additions to references on MR Safety, Books on Analysis, etc
  • 5

    2024 Martinos Connectivity Course Special Lecture by Michael D. Fox

    • Intro and Clinical Applications of Resting State Functional Connectivity MRI (Michael D. Fox; Nov 4, 2024)

    • Video of Michael D. Fox Lecture October 23, 2023
  • 6

    Day 1 Lectures and Homework Assignments

    • Welcome Presentation

    • Multivariate Analysis and Functional Connectivity, by Robert Savoy

    • Introduction to The CONN Toolbox

    • Preprocessing in CONN21

    • Exercises for Day 1

    • Video. Welcome Presentation

    • Video. Introduction to the CONN toolbox

    • Video. Multivariate Analysis and Functional Connevtivity

    • Video. Preprocessing in CONN (1_4)

    • Video. Preprocessing in CONN (2_4)

    • Video. Preprocessing in CONN (3_4)

    • Video. Preprocessing in CONN (4_4)

    • Video. Office hour #1
  • 7

    Day 2 Lectures and Homework Assignments

    • Walkthrough CONN21: Setup

    • Denoising and First Level

    • Homework Assignment after Day 2: Denoising and First Level Analysis

    • Video. Setup (1/4)

    • Video. Setup (2/4)

    • Video. Setup (3/4)

    • Video. Setup (4/4)

    • Video. Denoising & QC (1/2)

    • Video. Denoising & QC (2/2)

    • Video. Office hour #2
  • 8

    Day 3 Lectures and Homework Assignments

    • First-level analyses: SBC, RRC

    • (generalized) PsychoPhysiological Interactions (gPPI)

    • ICA (Independent Component Analysis)

    • Second Level (Group Analysis)

    • Second Level (Group Analysis) examples

    • Homework Assignment after Day 3: Group Level Analyses

    • Video. Homework assignment discussion

    • Video. First-level analyses. SBC and RRC

    • Video. Independent Component Analyses (ICA)

    • Video. Generalized Psycho-Physiological Interactions (gPPI)

    • Video. Misc. questions on ICA and gPPI

    • Video. Second-level analyses: General Linear Model (GLM)

    • Video. Second-level analyses: Contrast specification and examples

    • Video. Office hour #3
  • 9

    Day 4 Lectures and Homework Assignments

    • Alfonso's notes on the Homework Assignment from Day 3

    • Applications of Resting State Functional Connectivity Analysis by Dr. Susan Whitfield-Gabrieli.

    • Cluster Statistics

    • Homework Assignment after Day 4

    • Video. Homework 3 discussion

    • Video. Clinical applications of CONN, by Susan Whitfield-Gabrieli

    • Video. Cluster-level statistics (1/3)

    • Video. Cluster-level statistics (2/3)

    • Video. Cluster-level statistics (3/3)

    • Video. Office hour #4
  • 10

    Day 5 Lectures and Homework Assignments

    • GraphTheory (also called in this course, "Connectome Analysis")

    • Voxel to Voxel Analysis

    • MVPA: Multi-Variate Pattern Analysis

    • Dynamic Connectivity Analysis

    • Surface Based

    • CONN Parallelization options

    • CONN Scripting

    • General, End-of-Workshop Discussion

    • Video. Homework 4 discussion

    • Video. Graph theory

    • Video. Multivariate Pattern Analyses (fc-MVPA)

    • Video. Voxel to Voxel analyses

    • Video. Dynamic connectivity analyses (dyn-ICA)

    • Video. Parallelization and HPC options in CONN

    • Video. CONN Scripting and closing remarks
  • 11

    Some informal extra material

    • Resting State Connectivity Overview by Susan Whitfield-Gabrieli

    • References from Resting State Connectivity Overview Lecture

    • Additional references. To appear in book "fMRI techniques and protocols" (pre-print: Nieto-Castanon, A. (2022). Preparing fMRI Data for Statistical Analysis. arXiv. doi:10.48550/arXiv.2210.13564)

    • Additional references. "Demonstrating Quality Control (QC) Procedures in fMRI"