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: renzohuber@gmail.com or faruk.gulban@maastrichtuniversity.nl

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): https://maastrichtuniversity.zoom.us/meeting/register/tJAvcu-qpj8sHNVD71Vcu95et-R14QKRs22T

Objective(s):
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.
  - [Preparation reading] Helms, G. (2016). Segmentation of human brain using structural MRI. Magnetic Resonance Materials in Physics, Biology and Medicine, 29(2), 111–124. [or download from here]
- [4:30pm] Discussing preparation for next week: installing LAYNII, and downloading data.
Tuesday July 21st, LAYNII Tutorial
- [3:00-3:30pm, Faruk] Continuation of segmentation.
- [3:30-4:30pm, Renzo] Click/code-along LAYNII tutorial for generating layers.
  - Preparation:
    - Install LAYNII from github, e.g. with these https://layerfmri.com/laynii-setup/.
    - Download example data from Open neuro: https://openneuro.org/datasets/ds002274/versions/1.0.2. Alternative download link: here.
    - It is vital to have a nifty viewer installed. E.g. ITK-snap or FSLeyes or FSLfiew.
    - It would be very helpful to have AFNI installed too.
    - Useful commands:
  - Useful links:
    - How many layers to reconstruct: blog post here
    - Which layering algorithm to use: blog post here and here
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)