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Additional Resources

For those wanting to develop their learning beyond the scope of the module, here is a (non-exhaustive) list of links and pages for neuroscientists covering skills related to working with neuroimaging data, both with the concepts and practical application.

Contributing to the list

Feel free to suggest additional resources to the list by opening a thread on the GitHub page!

FSL Wiki

Most relevant to the course is the FSL Wiki, the comprehensive guide for FSL by the Wellcome Centre for Integrative Neuroimaging at the University of Oxford.

Existing lists of resources

Here are some current 'meta-lists' which already cover a lot of resources themselves:

  • Methods in Neuro Steven Weisberg's GitHub extensive list of resources covering the physics of MRI/fMRI, computational/programming, tools for the analysis of MRI/fMRI data, and online datasets, as part of his 'Methods in Neuroimaging' course at the University of Florida.
  • Hitchhacker's guide to the brain A 'docs' style website with lists of resources for each stage of neuroimaging analysis including file organisation, planning. preregistration, data collection, pre-processing and analysis, and sharing data. By Remi Gau, McGill University and others.
  • On-line neuroimaging resources A farily comprehensive list of 'softwares, databases, tutorials, blogs and other resources relevant to learn about neuroimaging or to help perform neuroimaging analysis'. Curated by Remi Gau, McGill University.
  • Dartbrains A notebook style introduction to neuroimaging in Python. The materials cover how scanner generates data, how psychological states can be probed in the scanner, and how this data can be processed and analyzed. Created by Luke Chang, Dartmouth College.
  • Awesome Magnetic Resonance Imaging (MRI) 'A curated list of delightful Magnetic Resonance (MR) courses, books, lectures, papers, blogs and free resources.' Created by Daniel Gomez, Harvard/MIT.
  • Awesome Neuroscience 'A curated list of awesome neuroscience libraries, software and any content related to the domain.' Created by Akash Tandon.
  • fMRI-Resources A GitHub list not dissimilar to this one, providing information and resources on functional MRI. Created by John Pyles.

Neuroimaging

Conceptual understanding

Struggling to grasp the fundamentals of MRI/fMRI? Want to quickly refresh your mind on the physiological basis of the BOLD signal? Well, these resources are for you!

  • Principles of fMRI The OG YouTube series for understanding the conceptual basis of MRI/fMRI. Created by Martin Lindquist and Tor Wager of Dartmouth College.
  • Neuroimaging Research Methods Another YouTube channel for learning about MRI/fMRI including research methods. Created by Rasmus Birn, University of Wisconsin-Madison.
  • Introduction to Principles of MRI A short book and associated simulation code for learning the principles of magnetic resonance imaging (MRI). Created by Peder Larson for students at UCSF.
  • Questions and Answers in MRI Ever had a question about the basis of MRI/fMRI? Written from the perspective of a physicist, this website was specifically made to answer these questions. Created by Allen Elster, Washington University School of Medicine.
  • fMRI Bootcamp A lecture series on fMRI, both conceptual and methodological by Rebecca Saxe, MIT.
  • MIT 9.13 The Human Brain, Spring 2019 A course which 'surveys the core perceptual and cognitive abilities of the human mind and explores how they are implemented in the brain'. Delivered by Nancy Kanwisher, MIT.

Analysis of fMRI data

  • Introduction to Working with MRI Data in Python A Software Carpentries course covering MRI file types, organisational formats (e.g., BIDS) and working with open datasets.
  • Andy's Brain Book The OG of neuroimaging tutorials. I don't know many trainee neuroimagers who haven't used Andy's amazing guides. Highly recommended to also check out his YouTube channel as well. Created by Andrew Jahn, University of Michigan.
  • NI-edu A website covering two courses, “fMRI-introduction” (basic concepts and methodology of functional MRI (fMRI) research) and “fMRI-pattern-analysis” (machine-learning based ‘decoding’ and representational similarity analysis (RSA)), which are in a notebook format. Created by Lucas Snoek, University of Amsterdam.
  • U of A: Neuroimaging Core Documentation Docs covering a range of neuroimaging tutorials including BIDS, ANTS, FSL, ITK-SNAP and more. Created by Dianne Paterson, University of Arizona.
  • Data analysis for Neuroimaging (DAFNI) Denis Schluppeck's materials for the MSc Cognitive Neuroscience course at the University of Nottingham, covering SPM, git, FSL and MATLAB.
  • Practice and theory of brain imaging A comprehensive course on neuroimaging in Python, with modules on reproducibility in programming/neuroimaging. Created by the Nipraxis team (Matthew Brett, Chris Markiewicz, Oscar Estaban, Zvi Baratz, Peter Rush).
  • Psych 214 – functional MRI methods A 'hands-on course teaching the principles of functional MRI (fMRI) data analysis' created for students at UC Berkeley by Matthew Brett and JB Poline.

Programming

Unix/Linux

Textbooks