Cookies on this website
We use cookies to ensure that we give you the best experience on our website. If you click 'Continue' we'll assume that you are happy to receive all cookies and you won't see this message again. Click 'Find out more' for information on how to change your cookie settings.
Graduate programme 2018
2017 students of the Graduate Programme

The FMRIB Graduate Programme is a set of courses designed to teach new researchers the theory and practice of MRI neuroimaging, from introductory courses on neuroscience and statistics, to MRI physics and analysis. It is an internal course available to students/postdocs/staff at the University Oxford and a limited number of nearby external registrants.  The programme is compulsory for new students at the FMRIB Centre. To date, over 300 participants have completed the Graduate Programme. Places are limited and, if necessary, are assigned according to need, with a signup process occurring in late summer.

It combines lectures with computer-based practicals, tutorials and demonstrations on the scanners. The core components are MR Physics and MRI Analysis, with additional modules on mathematics, neuroscience, IT and communications. 

The course takes place in various locations on the John Radcliffe Hospital site (see directions below). The course runs in all three University terms: Michaelmas, Hilary and Trinity. The larger courses in the programme are assessed by regular weekly short assignments and written exams.

OVERVIEW

The courses on the FMRIB Graduate Programme combine lectures/podcasts with computer-based practicals, tutorials and demonstrations on MRI scanners. The programme is suitable for students from a wide variety of backgrounds such as psychology, physiology, medicine, engineering, physics or mathematics.

The course comprises of three main components:

  • Introductory Course (Michaelmas term; 1st week - mornings, plus one optional afternoon)
  • Core Courses (Michaelmas, Hilary and Trinity terms)
  • Additional Modules (Michaelmas, Hilary and Trinity terms)

The core course is designed to give first-year DPhil students, or anyone new to the field of MRI research, a comprehensive introduction to the methods involved. Further education is provided through the Additional Modules and we recommend that attendees select an appropriate subset of modules, as suits their needs.

REGISTRATION

Registration for the 2017/18 course is now open. Please use this link to register: https://goo.gl/forms/MGM90JewJIcuHP3M2

Please note that registration includes three steps: i) fill out the questionnaire, ii) complete the online shop process (put the item in the basket *and* finalise the purchase), iii) receive a confirmation email from the online shop. If you have not received a confirmation email from Noreply.stores@admin.ox.ac.uk then your registration is NOT complete.

If you have any queries about the course then email graduate_admin@fmrib.ox.ac.uk .

TIMETABLE

The expected time commitment for the course is 6-8 hours per week, depending on options chosen.

See the timetable for the 2017-2018 academic year (subject to change).

The lecture and practical venues listed on the timetable can be found using the instructions and maps below.

BACKGROUND

The Oxford Centre for Functional Magnetic Resonance Imaging of the Brain has been involved in training graduate students since it opened in 1997. In 2003 the training was formalized to form the first FMRIB Graduate Programme. Over the years the course has changed to meet the needs of the broad range of students involved in MR imaging. In 2007 the course was significantly restructured to increase the level of tutor and practical work in the course, and introduced the very popular ‘Introduction to fMRI’ training week in the first week of the Autumn Term. In 2009 an Advanced Methods Programme was introduced specifically for students with a background in physical sciences, in order to cover some basic material on biological and medical science as well as more in-depth coverage of some physics and analysis topics. In 2014 podcasts of lectures were introduced and extra tutorial and practical material introduced into the core courses.

INDIVIDUAL COURSE DESCRIPTIONS

INTRODUCTION TO neuroimaging with mri (1ST WEEK of michaelmas term)

This intensive one-week course, organised by Prof. Mark Jenkinson and Prof. Jill O'Reilly, will introduce students to some of the tools and concepts essential for neuroimaging research. Participants will be introduced to the basics of imaging neuroscience, physics and analysis, including some applications of fMRI. Hands-on practical sessions will include the analysis of some fMRI data. The week also includes a practical component where students will perform a small fMRI study, including designing the experiment and acquiring the data.

reboot camp weeks (1st week of both hillary and trinity terms)

These intensive one-week courses are intended to kick-start the second and third terms. Session typically include:

  • Workshops on scientific computing (organised by Dr Falk Eippert and Prof Mark Jenkinson), that aim to introduce different software tools (such as UNIX and Matlab) at a very basic level. No prior knowledge of computing or individual software packages is assumed. 
  • Lectures and practicals on data, stats and maths (organised by Prof Saad Jbabdi, Prof Jill O'Reilly and Dr Jesper Andersson) that introduce the essential mathematical concepts for those doing neuroimaging. Aimed specifically at those who did not do a mathematical degree, as well as those with a mathematical background but without experience in using statistics in practice. It is based around examples that show how statistics and mathematics connects with daily practice when collecting, analysing and interpreting data, with a special focus on neuroimaging.
  • Talks on best practice in Neuroimaging (organised by Dr Janine Bijsterbosch & Prof Mark Jenkinson), that provide an introduction to researchers new to scanning in Oxford. These sessions include talks on the practicalities of scanning at Oxford, including topics such as: requirements to scan, interaction with radiographers, interaction with physicists, ethics, research in practice talks etc.

CORE GRADUATE PROGRAMME

The core graduate programme consists of three components, each integrating a number of teaching methods (including 1.5 to 2 hour podcasts), and aims to give students a thorough ‘hands-on’ understanding of the topic as well as the theory. It is aimed at a basic to intermediate level, is intended to be taken as a whole, and requires students to register and pay the course fee. 

MRI PHYSICS (BASIC LEVEL)

This course, organised by Dr Tom Okell and Dr Mark Chiew, aims to give students a background on how MRI data is acquired, and is run in Michaelmas term. One major goal is to enable researchers to make informed decisions about different aspects of their experimental protocols and the implications of these decisions on the resulting data quality. The first half of the course describes the basic physics underlying MRI acquisition and the second half focuses on the neuroimaging methods most commonly employed in Oxford, with particular focus on functional and diffusion MRI. No physics expertise is assumed. 

MRI ANALYSIS (BASIC LEVEL)

Organised by Prof. Mark Jenkinson and Dr Janine Bijsterbosch, this course will introduce the principles and practice behind the analysis of MR images, and is run in Hilary and Trinity terms. This includes image registration, segmentation, detecting structural changes, fMRI analysis and diffusion imaging. The theoretical lectures will be accompanied by tutorials and computer-based practicals using the FSL software package.  No prior analysis or mathematical skills (beyond school-level maths) are assumed.

ASSESSMENTS AND TIME COMMITMENT:

The two main courses, MR physics and MRI analysis, each include weekly short practical exercises with questions to be answered, and an end of term exam. Most students should expect to spend 1-2 hours a week viewing podcasts, going over material and preparing for tutorials/practicals in addition to the formal contact hours (typically 2-4 hours per week) for the core courses. 

ADDITIONAL MODULES

In addition to the main programme there are supplementary courses that anyone is welcome to attend (for free). These span a range of levels from basic to intermediate and advanced levels. The intended audience and level is described for each course below. Advanced level courses vary from year to year and are primarily aimed at methods students (physics/analysis), but are expected to also be useful for interested second- and third-year students with a clinical or neuroscience background, once they have gained some practical experience in neuroimaging.  Most first-year students would benefit from attending 50-70% of these module sessions.

INTRODUCTION TO NEUROSCIENCE (BASIC LEVEL, Michaelmas term)

This course, organised by Dr Rogier Mars and Dr James Kolasinski, will give students without a biomedical background (e.g., physicists and engineers) an introduction to some key topics in neurology and neuroscience. The focus is on physiological and psychological processes that neuroscientists are interested in, and the limitations of the current methods for measuring them. Topics covered include: Grey matter anatomy and cerebral vasculature; Anatomy of the white matter; Cellular signalling; Brain chemicals; and the Physiology of blood vessels and its relation to BOLD.

ADVANCED MR PHYSICS (ADVANCED LEVEL, hillary term)

This course, organised by Dr Tom Okell, will cover selected topics in MRI physics to a level beyond that covered on the core graduate programme. A more mathematical and equation-based treatment of topics will be used.

ADVANCED MATHS AND ANALYSIS (ADVANCED LEVEL, hillary term)

This course, organised by Prof. Saad Jbabdi, introduces key mathematical concepts behind much of the research and software of the Image Analysis Group, to a level beyond that covered on the core graduate programme. A more mathematical and equation-based treatment of topics will be used. Topics covered include: Bayesian Modelling; Optimisation; Uni-variate Statistics & Time-Series Analysis; Multi-variate Modelling & Analysis; and Resting-State Analysis & ICA.

ANALYSIS AND INTERPRETATION (BASIC - INTERMEDIATE LEVELS, TRINITY TERM)

This course, organised by Prof. Gwenaelle Douaud, will cover the ways in which analysis results should and should not be interpreted.  It focusses on diffusion and functional analysis and examines both clinical and non-clinical research.  Best practice tips and known pitfalls are highlighted, with examples provided from the literature. Knowledge of analysis and physics, as covered by the core courses, is assumed.

HOW TO GET TO THE JR HOSPITAL SEMINAR ROOMS AND LECTURE THEATRES

All of the lectures and practicals on the FMRIB Graduate Programme take place somewhere in the John Radcliffe Hospital site.

There are a variety of venues on this site, as listed here (with maps):

ADDITIONAL INSTRUCTIONS FOR ACCESS TO LEVEL 6, WEST WING

Access is restricted to the Level 6, West Wing seminar rooms, and so you will need to read the following instructions to be able to get through:

TO GET TO THE LEVEL 6, WEST WING SEMINAR ROOMS FROM THE CHILDREN'S HOSPITAL ENTRANCE:

  1. Take the lifts to Level 2.
  2. Out of the lifts go through the doors straight ahead and turn left to the end of the corridor.
  3. On your left are a set of double doors with swipecard only access.
  4. Follow the instructions "From Level 2 Intercom" below.

TO GET TO THE LEVEL 6, WEST WING SEMINAR ROOMS FROM THE MAIN HOSPITAL ENTRANCE:

 

  1. Pass the main reception desk and follow the corridor towards CHILDREN'S HOSPITAL / WEST WING. En route you will pass on your right hand side a bank machine, a small supermarket and the League of Friends cafe.
  2. Proceed past the League of Friends cafe and continue on straight ahead.
  3. You should now be facing a set of double doors with swipecard only access.
  4. Follow the instructions "From Level 2 Intercom" below.

FROM LEVEL 2 INTERCOM:

  1. Press the BELL on the INTERCOM at this entrance and await LEVEL 6 reception to reply.
  2. Speak into the intercom camera and please clearly announce your name and department and state that you are attending the FMRIB Graduate Program.
  3. Upon passing through a second set of double doors directly ahead of you, turn immediately RIGHT and immediately RIGHT again into the LIFT LOBBY. (Do not use "FM lift only").
  4. Enter the lift and get off at LEVEL 6.
  5. At level 6 press the intercom system at the LEVEL 6 ENTRANCE and you will be allowed into reception and directed to the Seminar room.

Contact

If you have any questions about the programme then please feel free to contact any of the course organizers or the course administrator at graduate_admin@fmrib.ox.ac.uk

Notes & Resources

For students registered on the programme, lecture notes and other resources can be found on the WebLearn site (note that Oxford students will require an OUCS account for access).