Contents of book

Open
#1 15 comments 2 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
20/100
Issue type
Documentation
Clarity
Needs clarification
Activity status
Stale
Tech stack
tex
Domain
documentation

Research direction

No files or tests are named. Start by reviewing the proposed book sections, linked dual-echo and cerebrovascular-reactivity resources, and the tedana, t2smap, nilearn, and AFNI topics. Done requires an agreed scope and completed, coherent content for the selected sections.

Written by the indexing model from the issue text.

Description

Just a few initial thoughts:

  1. Getting started
    1. Download data
      • Download fMRIPrepped multi-echo data using tedana datasets module. Probably just one run from the Cambridge dataset and something that's compatible with dual echo denoising (i.e., first echo <= 5ms).
      • Download dual-echo data as well.
    2. Software installation
    3. Recommended reading
      • Papers on multi-echo denoising
      • Paper on dual echo denoising
      • At least one paper on BOLD-based physiological noise
  2. Theoretical Background
    1. A primer on MR physics
    2. Single- and multi-echo fMRI
      • With sequence diagrams
    3. Signal decay
      • The monoexponential model, T2* and S0
      • Information on other models of signal decay
    4. BOLD, non-BOLD, and TE-dependence with tedana
      • Building an intuitive understanding of T2* and S0 with gifs
  3. Practical Resources
    1. Available multi-echo datasets
    2. Acquiring multi-echo data
    3. Processing multi-echo data
  4. Analysis tutorials
    1. Optimal combination with t2smap
      • How does optimal combination improve coverage and increase SNR
    2. Multi-echo denoising with tedana
      • tedana's approach
      • Dependence metrics
      • Group-level analysis (e.g., applying transforms)
    3. Dual echo data
      • Just with some nilearn code. Should be easy enough to do first echo-regression.
    4. 3dMEPFM
    5. Cerebrovascular reactivity mapping
  5. Other possible analyses
    1. Dynamic distortion correction (requires phase data)
  6. Contributing tutorials
  7. Glossary
Dominant language
TeX
Stars
6
Forks
4
No merged PRs in 30d

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

More from ME-ICA/multi-echo-data-analysis

All issues in ME-ICA/multi-echo-data-analysis

Similar issues

More Documentation issues

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.