October 2-5 2023 @ Martinos Center in Boston, MA 

The combination of ultra-high field (7 Tesla and above) imaging with increasingly sophisticated data analysis tools has led to a surge of research using functional MRI acquisitions to examine the behavior of individual cortical layers of the brain. This course will focus on teaching the acquisition and analysis tools needed to contribute to this research.    

Content: four days of hands-on training on laminar fMRI
day 1: introduction to laminar fMRI & basic data acquisition
day 2: data preprocessing and analysis
day 3: interpretation and modeling
day 4: advanced applications and future directions

Organizers: Jonathan Polimeni [course director],
Anna Blazejewska, Laurentius (Renzo) Huber & Robert Savoy

Course Faculty: Peter Bandettini, Anna Blazejewska, Saskia Bollmann, Jingyuan Chen, Anna Devor, Jozien Goense, Daniel Gomez, Doug Greve, Faruk Gulban, Laurentius (Renzo) Huber, A. Tyler Morgan, David Norris, Jonathan Polimeni, Robert Savoy, Kamil Uludag, Divya Varadarajan, Luca Vizioli

Day 1 (Oct 2, 2023)

Topic I: Introduction to laminar fMRI

Program Overview – Jon Polimeni

Theory: What Neuroscience Insights can Layer-Specific Activity Provide? – Jozien Goense

What is a cortical layer? Cyto-, Myelo-, Angio- and Functional Architecture – Jon Polimeni

Applications of Laminar fMRI: History, Key Applications, and Lessons Learned – David Norris

Topic II: Basic Data Acquisition

Basic Laminar fMRI Acquisition Toolkit (Functional and Anatomical Pulse Sequences) – Saskia Bollmann

Practical Aspects of High-Resolution Functional protocol optimization and data acquisition – Renzo Huber

High-Resolution Anatomical (and Vascular) Data Acquisition – Saskia Bollman

Day 2 (Oct 3, 2023)

Topic III: Data Preprocessing and Analysis

Summary of Day 1 – Jon Polimeni

Laminar fMRI Data Analysis Overview – A. Tyler Morgan

Cortical Segmentation I: Whole-brain and automatic methods – Daniel Gomez

Cortical Segmentation II: Partial-brain methods and quality control – Faruk Gulban

Accurate Functional-Structural Registration, Alignment, and Validation – Doug Greve

EPI Distortion Correction – Divya Varadarajan

High-Resolution fMRI Data Preprocessing – Jon Polimeni

Denoising: getting past the thermal noise barrier using NORDIC – Luca Vizioli

Physiological Noise across layers – Jingyuan Chen

Cortical Partial Volume Correction and “Spatial GLM” for Resolving Layers – Doug Greve

Day 3 (Oct 4, 2023)

Topic IV: Interpretation and Modeling

Summary of day 2 – Jon Polimeni

Principles and Algorithms: Into The Depths of Layers, Layerification, And Laminar Hypothesis Testing – Faruk Gulban

Visualization: Laminar Profiles, Informed Smoothing, and Cortical “Flattening” – Anna Blazejewska

Hands-on I: From EPI activation to layer-profiles in LayNii – Renzo Huber

Hands-on II: “When I tried it, it didn’t look as nice as on your slides” – Renzo Huber

Laminar Functional Connectivity – Jingyuan Chen

Interpreting Cortical Depth-Dependent fMRI Signals: Biophysical Models and Inversion – Kamil Uludag

How to Publish Your Laminar fMRI Study: What do Reviewers Want to See? – Jon Polimeni & Renzo Huber

Day 4 (Oct 5, 2023)

Topic V: Advanced Applications and Future Directions

Summary of day 3 – Jon Polimeni

Neuronal Specificity of Hemodynamics and Neurovascular Coupling: What is Known? – Anna Devor

Advanced Analyses and Computational Modeling in layer-fMRI – Luca Vizioli

Keynote Lecture:

Future Directions: Will Laminar fMRI Change Human Neuroscience? – Peter Bandettini

General Discussion; Additional Resources; Class Review and Feedback – Jon Polimeni & Renzo Huber