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Course Details
A following gives a description of each of the courses offered in the 2011/12 program
Introduction to FMRI (1st week)
This intensive one-week course, organised by Dr Mark Jenkinson, 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. The week includes a significant practical component where
students will perform a small fMRI study, starting from designing the
experiment, and continuing through to implementation, acquisition, and
analysis of the experimental data.
Core Graduate Program (Mondays)
The core graduate program consists of three components, each integrating a number of teaching methods, 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 and is intended to be taken as a whole.
MRI Physics (Basic Level)
This course, organised by Dr Karla Miller, aims to give students a background on how MRI data is acquired. 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 Dr Mark Jenkinson, this course will introduce the principles and practice behind the analysis of MR images. 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. The course also includes a project where a full, multi-subject fMRI analysis is performed on experimental data.
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. In the MRI analysis course there is also a more substantive project, lasting several weeks, and requiring a journal-style written report. The average time commitment expected from students is an additional 2-3 hours during the week outside the lecture/practical slot.
Methods Teaching Program (Thursdays)
In addition to the main program there are supplementary courses that anyone is welcome to attend. 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 expected to also be useful for many second- and third-year students with a clinical or neuroscience background, once they have gained some practical experience in neuroimaging.
Easy Maths (Basic Level)
This course, organised by Dr Saad Jbabdi, introduces the essential mathematical concepts for those doing neuroimaging, aimed specifically at those who did not do a mathematical degree. It is based around examples that show how the mathematics connects with daily practice when collecting, analysing and interpreting data.
Scientific Communication (Basic Level)
All scientists need to be able to present their work effectively, both orally, and in writing. This set of lectures and practical workshops, organised by Dr Clare Mackay, gives participants the opportunity to review their writing and presentation, to increase in confidence for communicating scientific work. The sessions focus on being able to produce good written work and talks specifically for conference abstracts, posters and journal papers.
Introduction to Neuroscience for Physicists and Engineers (Basic Level)
This course, organised by Dr Charlotte Stagg and Dr Jill O’Reilly, will give students without a biomedical background 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.
IT skills (Basic Level)
This course, organised by Dr Duncan Mortimer and Dr Mark Jenkinson, aims to introduce different software tools at a very basic level, via a series of workshops. No prior knowledge of computing or individual software packages is assumed. Topics: Introduction to UNIX; Data Management; Introduction to MATLAB; Introduction and Intermediate Scripting; Introduction to (stimulus) 'Presentation'.
Advanced MR physics (Advanced Level)
This course, organised by Dr Karla Miller, will cover selected topics in MRI physics to a level beyond that covered on the core graduate program. A more mathematical and equation-based treatment of topics will be used.
Advanced Maths and Analysis (Advanced Level)
This course, organised by Dr Mark Jenkinson and Dr 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 program. 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.