layer-fMRI Webinar MBIC 2020

Title: High resolution fMRI: An introductory course for data acquisition and analysis challenges.

Support: This lecture series is finanzially supported by the FPN-MBIC-school. The session on sequences and sequence artifacts is supported (in kind) by the York-Maastricht-partnership grant. Faruk Omer Gulban works for Brain Innovation.

Coordinators: Laurentius (Renzo) Huber & Omer Faruk Gulban, Cognitive Neuroscience Department

Email: or

Dates: 7, 14, 21, 28 July 2020 (4 sessions in total), 3pm to 4:30pm.

Video Conference Zoom link (note that these sessions may be recorded):

This course will be an introduction to acquiring and analyzing high resolution (<1mm) functional magnetic resonance imaging (fMRI) data. The course participants will acquire data and analyze with the guidance of the course coordinators.

After this course, participants will be able to:

  • Give a rough overview of the seminal papers, challenges and prospects of laminar fMRI
  • Discuss the most common artifacts at the scanner and how to address them
  • Make more informed decisions for their own high resolution fMRI acquisitions.
  • Use image registration and segmentation methods to address some of the most challenging analysis steps.

Literature: There will be no textbook. Individual articles will be suggested for the sessions 3 and 4.

Form of assessment: Attendance (all 4 sessions).

Detailed schedule

  • Tuesday July 7th, 3pm-5:30pm, Introduction

    • [3:00-3:30pm] Getting to know each other
    • [4:30-4:00pm] Introduction lecture from Faruk
    • [4:00-4:30pm] Introduction lecture from Renzo about the layer-(f)MRI field
    • Divisions of projects (see table below), topics can be:
      • A paper chosen from this list of papers.
      • A software presentation.
      • A presentation from their PhD project.
      • List of topics below.
  • Tuesday July 14th, High-res EPI scanning tutorials and artifacts (virtual)

    • [3:00-4:00pm, Renzo] Virtual 7T MRI scan session.
      • Step-by-step optimizing sub-millimeter fMRI.
      • Optimizing GRAPPA parameters.
      • Detecting and correcting high-res EPI artifacts.
      • TR, coverage and resolution trade-offs.
      • Phase encoding direction GRAPPA artifacts.
      • Anatomical sequences for 0.5 mm resolution.
    • [4:00-4:30pm, Faruk] Segmentation of 7T MR images. 
    • [4:30pm] Discussing preparation for next week: installing LAYNII, and downloading data.
  • Tuesday July 21st, LAYNII Tutorial

  • Tuesday July 28th, 3:00pm-5:30pm, Attendees give 8min presentations 

    1. Logan: Methods to correct for venous biases in GE-BOLD.
    2. Yawen: Brightness induction.
    3. Miriam: Odd-ball detection.
    4. Kirsten: High-level feedback to V1.
    5. Johannes: Paper discussion of Peter Koks Kanizsa triangle study.
    6. Dominika: Paper discussion of Andrew Persichetti’s imaginary finger movement study.
    7. Minye: EPI distortion correction and individual differences.
    8. Ceren: Deep brain structures for auditory perception. (canceled)
    9. Marco: Multi-sensory motion perception. (canceled)

Survey from FPN/CN:


Introduction of the course

Introduction to layer-fMRI

  • Hands on segmentation:
  • Participants contributions:
    • Logan: Methods to correct for venous biases in GE-BOLD
    • Yawen: Brightness induction.
    • Miriam: Odd-ball detection.
    • Minye: EPI distortion correction and individual differences.

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