MRI on BEAR

MRI on BEAR is a collection of educational resources created by members of the Centre for Human Brain Health (CHBH), University of Birmingham, to provide a basic introduction to fundamentals in magnetic resonance imaging (MRI) data analysis, using the computational resources available to the University of Birmingham research community.

About this website

This website contains workshop materials created for the MSc module 'Magnetic Resonance Imaging in Cognitive Neuroscience' (MRICN) and its earlier version - Fundamentals in Brain Imaging taught by Dr Peter C. Hansen - at the School of Psychology, University of Birmingham. It is a ten-week course consisting of lectures and workshops introducing the main techniques of functional and structural brain mapping using MRI with a strong emphasis on - but not limited to - functional MRI (fMRI). Topics include the physics of MRI, experimental design for neuroimaging experiments and the analysis of fMRI, and other types of MRI data. This website includes only the workshop materials, which provide a basic training in analysis of brain imaging data and data visualization.

Learning objectives

At the end of the course you will be able to:

• Demonstrate an understanding of the basic concepts involved in MRI
• Show an understanding of how to design fMRI experiments
• Have the ability to work with BlueBEAR in a Linux environment and to use appropriate software to view and interpret MRI data
• Be able to analyse simple fMRI experiments and conduct basic tractography analysis

For externals not on the course

Whilst we have made these resources publicly available for anyone to use, please BEAR in mind that the course has been specifically designed to run on the computing resources at the University of Birmingham.

Teaching Staff

Dr Magdalena Chechlacz

Role: Course Lead

Magdalena Chechlacz is an Assistant Professor in Cognition and Ageing at the School of Psychology, University of Birmingham. She initially trained and carried out a doctorate in cellular and molecular biology (2002). After working as a biologist (Larry L. Hillblom Foundation Fellowship at the University of California, San Diego) she decided on a career change to a more human-oriented science and neuroimaging. In order to gain formal training in cognitive neuroscience and neuroimaging, she completed a second doctorate in psychology at the University of Birmingham under the supervision of Glyn Humphreys (2012). From 2013 to 2016, she held a British Academy Postdoctoral Fellowship and EPA Cephalosporin Junior Research Fellowship, Linacre College at the University of Oxford. In 2016, Dr Chechlacz returned to the School of Psychology, University of Birmingham as a Bridge Fellow.

Aamir Sohail

Role: Teaching Assistant

Aamir Sohail is an MRC Advanced Interdisciplinary Methods (AIM) DTP PhD student based at the Centre for Human Brain Health (CHBH), University of Birmingham, where he is supervised by Lei Zhang and Patricia Lockwood. He completed a BSc in Biomedical Science at Imperial College London, followed by an MSc in Brain Imaging at the University of Nottingham. He then worked as a Junior Research Fellow at the Centre for Integrative Neuroscience and Neurodynamics (CINN), University of Reading. Outside of research, he is also passionate about facilitating inclusivity and diversity in academia, as well as promoting open and reproducible science.

Course Overview

Workshop	Key Concepts/Tools
Getting Started	BEAR Portal, BEAR Storage, BlueBEAR
Workshop 1	BlueBEAR GUI, Linux commands, Terminal basics
Workshop 2	NIFTI/DICOM format, FSLeyes viewer, MRI atlases
Workshop 3	DTI preprocessing, DTIfit, TBSS, BET
Workshop 4	Probabilistic tractography, BEDPOSTX, PROBTRACKX
Workshop 5	Advanced BET, FEAT, First-level fMRI analysis
Workshop 6	Bash scripting, Submitting jobs, Containers
Workshop 7	Group-level fMRI analysis, Fixed/Random effects
Workshop 8	Resting-state fMRI, Functional connectivity, Neurosynth

Accessing additional course materials

If you are a CHBH member and would like access to additional course materials (lecture recordings etc.), please contact one of the teaching staff members listed above.