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Tutorials
Welcome to the tutorial page of Brainhack Western 2023! A short description of the tutorials being taught are available below.
The tutorials are currently not in any particular order.
- Diffusion (DTI) and functional (fMRI) MRI: imaging beyond structure
- Writing research impact statements: a micro workshop on drafting an elevator pitch
- Data mining: meta-analyses for neuroimaging data
- Research code management: best practices
- Research data management: from collection to sharing
- Data visualization: Designing and constructing informative graphics
- Reproducible data analysis with workflows
- Open science and data sharing in the context of Indigenous Research: a panel discussion
- A brief introduction to MRI
- Modern Realities of Behavioral Research
- Neuroanatomy for Researchers: a Focus on Surgical Targets
- Introduction to EEG
Organizers: Farah Mushtaha and Suzanne Witt
This joint tutorial will cover both the basics of diffusion MRI and functional MRI. For diffusion MRI, the basics of processing data from MRI acquisitions to computing diffusion tensors and tracking the structural connectome will be covered. For functional MRI, the basics of what aspect of brain function fMRI measures to considerations for preprocessing fMRI data will be presented.
Organizer: Suzanne Witt
This micro workshop (based on MIT's Impact course) will cover what an impact statement is in the context of research. Most of the workshop will be devoted to attendees working in small groups drafting impact statements for their own research suitable for the proverbial elevator pitch or meet-and-greet scenarios.
Organizer: Suzanne Witt
Meta-analyses of neuroimaging data are a good way to get started with understanding neuroimaging and task-based neural processing, as well as, answer research questions that may not be easily addressed with by traditional data collection. This tutorial will cover the various aspects of designing a meta-analysis and some of the more popular methods, including both topic- and contrast-based meta-analyses and coordinate- and image-based meta-analyses. Some hands-on work with the python-based tool NiMARE with a sample dataset will be included to help attendees appreciate some of the nuances between the various types of meta-analyses. A new, web-driven all-in-one meta-analysis toolbox will also be introduced.
Organizers: Suzanne Witt and Tristan Kuehn
This tutorial will cover best practices for managing research code with the ultimate goal of sharing it. Aspects of Git and GitHub, including version control, branching, collaborations, etc. will be covered. Additionally, new guidelines to help researchers assess how open and sharable their code is will be presented.
Organizer: Tristan Kuehn
Handling data can be a challenge, and it’s best to think about it before you need to organize it on a deadline. In this tutorial you’ll learn best practices for collecting, storing, processing, and sharing your data. We’ll go over writing a Data Management Plan, formatting your data with BIDS and other open standards, and version controlling your data with DataLad, and uploading to a public repository.
Organizer: Tristan Kuehn
A great data visualization can effectively demonstrate the arguments you’re making in a paper. In this tutorial you’ll learn about designing informative graphics, and how to use one of a selection of tools to combine your design and data into a paper-ready graphic. We’ll go over tools in Python, but most of the concepts should be transferable to your toolset of choice.
Organizers: Tristan Kuehn
Using a workflow management tool to run your research analyses can make it much easier to remember what you’ve done with your data, make small adjustments, and describe your analyses to others in a reproducible way. In this tutorial, you’ll learn about what a workflow management tool is, why you might want to use one, and how to write your analyses as workflows. As an example, we’ll go over SnakeBIDS, a Western-grown workflow management tool for handling BIDS-formatted neuroimaging data.
Organizers: Keza Motlana and Suzanne Witt
Panelists: TBA
The rules, guidelines, and obligations when it comes to conducting Indigenous Research are different in Canada than for non-Indigenous populations. Come learn about why these differences exist and how they relate to the open science and data sharing expectations that exist for much of neuroscience and neuroimaging research.
Organizer: Brad Karat
This tutorial will provide a basic introduction to MRI. We will cover where the MRI signal is originating from, what are the different contrasts, basic pulse sequences for acquiring an image, how to reconstruct and visualize an image from DICOM to NIFTI, and unique MRI contrasts such as diffusion or functional imaging.
Organizers: Priya Kalra and Anthony Cruz
This tutorial will cover the basics of behavioral data collection and analysis in neuroscience-adjacent fields such as cognitive psychology. The session will provide a broad overview of the topic, ranging from basics of behavioral experiment design, stimulus presentation, and data collection and analysis, to emerging data analysis techniques and online data collection. Throughout, the software options available for each step will be briefly discussed. No previous knowledge or experience is expected.
Organizer: Alaa Taha
In this tutorial, we will begin with a basic introduction to neuroanatomy then briefly discuss the hippocampus, basal ganglia structures, midbrain, and relatively uncharted zona incerta. Taking on a clinical lens, we will explore how these structures could be crucial targets during functional neurosurgical procedures.
We end our tutorial with 3 mini-software demo stations:
- learning neuroanatomy using an open and validated anatomical fiducial framework (AFIDs; https://validator.afids.io/),
- reviewing introduced anatomy in the context of a surgical case using a virtual reality headset, and
- applying our functional neuroanatomy knowledge to plan a surgical case using a fully open-source software (trajectoryGuide; https://trajectoryguide.greydongilmore.com/).
Organizer: Mauricio Cespedes Tenorio
This tutorial will explore the essentials of EEG, including its origin, conventions and related modalities. From there, we’ll step into the world of EEG analysis, from time domain to time-frequency analysis, all while getting hands-on sessions with Python. Finally, the tutorial will cover a bit on the important role of preprocessing in EEG. Discover the fascinating world of EEG with Python.