Instructor Notes

Scope of Lesson

The primary objective of this workshop is to introduce learners to basic fMRI concepts and to demonstrate an end-to-end analysis of functional imaging data using Python. The lessons are designed to walk a learner through each step of the fMRI analysis process with a series of hands-on notebooks.

Although the primary learning path presented is focused in on Resting State connectivity analyses, we recognize that it does not cover the vast scope of functional imaging analyses. As such, this workshop will be updated with modules (i.e task GLM) that will provide learners and instructors with additional learning paths. If you’re interested in proposing a sub-module/learning path for this workshop feel free to contact the workshop developers on the GitHub discussion board for this workshop.

Learner Pre-requisites

Intro to fMRI analyses is meant to be taught as part of a broader Neuroimaging carpentries lesson. As such, it makes some basic assumptions (although we provide very quick overviews) of concepts taught in the pre-requisite workshop: Intro to MRI. In addition, we expect learners to have some basic familiarity with Python (Software Carpentries provides such a workshop).

In summary the core pre-requisites that we expect learners to have some familiarity with are the following:

  • Basic Python programming knowledge
  • DataLad
  • BIDS and the pyBIDS for querying BIDS datasets
  • Introductory knowledge about NIFTI data: header, affine, array data, voxel resolution

Lesson Design for Instructors

Teaching Style

This workshop as originally designed to be a live-coding session where learners are walked through the process of cleaning and analyzing resting state fMRI data. To this end, all lessons in the carpentries have a mirror Jupyter Notebook codebook. Jupyter Notebooks can be found in the code directory of the git repo. Each episode in code/ mirrors the corresponding episode in the workshop’s carpentries site.

In addition, we provide two versions of each notebook i.e:

  • 02-exploring_fmriprep.ipynb
  • 02-exploring_fmriprep_solutions.ipynb

The notebook with a _solutions suffix contains pre-filled cells that can be used by the instructor as a reference when live-coding. In addition, any learners falling/running into issues may also reference the solutions noteobok to catch-up to the instructor.

The notebook without the _solutions suffix (“workshop notebook”) is mostly blank (aside from boilerplate code, and markdown text) and serves as the platform on which live-coding occurs. In addition, any exercise in the workshop notebook may contain template code that learners are expected to complete in a fill-in-the-blanks style problem.

Companion Slides

Companion slides are provided for instructors to provide visual aid during certain components of the workshop. We recommend that slides are used for the following episodes:

Slides 1-5 - Introduction

May be used in lieu of Episode 1 Introductory slides that present the goals of the workshop as well as give an overview of the material to be presented to the learners.

Slides 10-18 - Preprocessing

To be presented prior to Episode 2 These slides present an overview of fMRI pre-processing steps as well as motivation for its use prior to statistical analysis of fMRI. It also introduces the fMRIPrep pipeline as the recommended pre-processing pipeline - this is typically of interest to many learners from our experience. In addition, the data used in the workshop are outputs from the fMRIPrep pipeline.

Slides 19-20 - Confounds

To be presented prior to Episode 5 This slide presents a brief motivation behind the need for confound/nuisance regression in fMRI analysis.

Tips for hosting a successful workshop

  • From experience, the most difficult component of the workshop is the set-up process. It is highly recommended that learners use the workshop’s Binder image. It may be useful to set up a separate time-slot to focus on local set-up after the main workshop.
  • It is often helpful (wherever possible) to have multiple screens on display during the workshop:
    • one with the workshop live-coding notebook
    • one with a solutions notebook
    • This is helpful for learners falling behind
  • This workshop is sequentially dependent, if learners fail to run a preceding code block they will not be able to run subsequent blocks causing frustration. Try to ensure that any issues from learners get resolved as soon as it is brought up
  • We recommend additional helpers be available during teaching of the workshop. It is often easier to keep the pace/timing of the workshop when a helper is available to address minor issues learners may run into

Frequent Issues

  • Python Kernel Dies in Binder: This is a result of the limited memory available (2GB) available in each Binder instance. This can be prevented by shutting down a notebook once it is done with. Simply closing a notebook does not shut it down and will continue to take up memory!.
    • Another solution is to request additional resources from the Binder maintainers
    • The request form above can also be done to extend the timeout duration so that the connection isn’t lost during a break