UBC MRI Centre	Vancouver Hospital and Health Sciences Centre	Providence Health Radiology	University of British Columbia

The UBC Functional MRI Resource Page Alan Bates, MD, PhD Department of Psychiatry, University of British Columbia

General MRI Theory/Background	Functional MRI Theory/Background	Data Analysis Software
Stimulus Presentation Software	Local fMRI Research Groups/People	fMRI Research Groups Outside Vancouver
UNIX and LINUX	Brain Atlases	MRI Safety
General Statistics	Digital Signal Processing	General Image Processing
Imaging Societies	Computer Port Information	Commercial MRI Scanner Manufacturers
Funding Agencies	Journals

General MRI Theory/Background The Basics of MRI by Joseph Hornak Simply Physics MRI Introduction e-MRI (interactive MRI tutorial) ReviseMRI.com (includes quizzes) Basic principles of MRI (pdf document) - Wm. Faulkner MRI Tutor Website - Ray Ballinger The Adelaide MRI Website (lots of links) - Greg Brown Wikipedia Page on MRI Books: Quantitative MRI of the Brain: Measuring Changes Caused by Disease, by Tofts (Ed.) Woodward Library WL141.Q16 2003 Understanding Magnetic Resonance Imaging, by Smith and Lange Woodward Library QC762.6.M34 S65 1998 MRI: The Basics, by Hashemi, Bradley and Lisanti Woodward Library WN18.2.H384 2004 MRI Principles, by Mitchell and Cohen Woodward Library WN185.M583 2004 MRI at a Glance, by Westbrook Woodward Library WN185.W477 2002 MRI from Picture to Proton, by McRobbie, Moore, Graves and Prince Woodward Library WN185.M9386 2007 MRI in Practice, by Westbrook, Roth and Talbot Woodward Library WN185.W488 2005

Functional MRI Theory/Background An Introduction to fMRI by Bianca de Haan Stuart Clare's PhD Thesis on fMRI fMRI for Newbies, by Jody Culham FMRIB Introduction to FRMI MRI and fMRI Primer by Douglas Noll Overview of fMRI Analysis, S.M. Smith, British Journal of Radiology About Functional MRI, Columbia University Cambridge Cognition and Brain Sciences Unit Imaging Wiki Introduction to fMRI: Design, Analysis, and Interpretation, by James Danckert The fMRI Data Centre FunctionalMRI.org (good links for fMRI tutorials) fMRI for the Psychiatrist RadiologyInfo (basic description of fMRI for patients/participants) Wikipedia page on fMRI Books: Functional MRI: An Introduction to Methods, by Jezzard, Matthews and Smith (Eds.) Functional Magnetic Resonance Imaging, by Huettel, Song and McCarthy Woodward Library WN185 H888 2004 Functional MRI, by Moonen and Bandettini (Eds.) BMB Library WL300 F8538 1999 Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques, by Buxton Statistical Parametric Mapping: The Analysis of Functional Brain Images, by Friston (Ed.) Computing Brain Activity Maps from fMRI Time-Series Images, by Sarty Woodward Library WL335.S24 2007 The Statistical Analysis of Functional MRI Data, by Lazar Handbook of Functional Neuroimaging of Cognition, by Cabeza and Kingstone (Eds.) Woodward Library WL335 H353 2006 Functional MRI: Basic Principles and Clinical Applications, by Faro and Mohamed Clinical Functional MRI: Presurgical Functional Neuroimaging, by Stippich (Ed.) Clinical Applications of Functional Brain MRI, by Rombouts, Barkhof and Scheltens Functional MRI: Applications in Clinical Neurology and Psychiatry, by D'Esposito Woodward Library WL141.F8536 2006

Data Analysis Software Statistical Parametric Mapping (SPM) MarsBaR Region of Interest Toolbox for SPM Phiwave wavelet toolbox for SPM VBM Toolboxes, University of Jena SPM5 Batch Scripts SPM2 Manual from Columbia University (rough guidance for analysis of a block design) A Collection of SPM2 Batch Scripts, by Chris Rorden Adrien Desjardins' SPM99 Manual, from UBC, Adapted for use at the University of Nottingham Psychiatry Division FMRIB Software Library (FSL) Analyses of Functional Neuroimages (AFNI) FMRLAB by the SCCN (ICA analysis of fMRI data) BrainVoyager Curry MRIcro, MRIcron and other resources by Chris Rorden FreeSurfer XBAM by the Brain Image Analysis Unit, Institute of Psychiatry NIPY Neuroimaging Tools for Python FMRISTAT by Keith Worseley VoxBo, Center for Functional Neuroimaging, University of Pennsylvania FIASCO Brain Imaging Software Toolbox, McConnel Brain Imaging Centre, MNI fmripower (power calculations for fMRI) Automated Image Registration (AIR) by Roger Woods BrainVISA and Anatomist Group ICA Toolbox Lyngby fMRI Analysis Package by Pawel Skudlarski Van Essen Lab Brain Mapping Software Various Resources by Thomas Nichols

Stimulus Presentation Presentation by Neurobehavioral Systems Psychology Software Tools, makers of E-Prime SuperLab Cogent by the LON, FIL, and ICN FEST by FMRIB Cortex, NIMH Laboratory of Neuropsychology Visual and Auditory Presentation Package (VAPP) by Kent Kiehl and Tony Gray Display Master by K.I. Forster and J.C. Forster PsyScope Resonance Technology Avotec Adobe Audition

Local fMRI Research Groups/People UBC High Field MRI Centre (Director: Dr. Alex MacKay) Dr. Stella Atkins' Medical Computing Laboratory Dr. Jason Barton's Human Vision and Eye Movement Laboratory Dr. Alan Bates, UBC Department of Psychiatry Dr. Bruce Bjornson, Neurosciences, BC Children's Hospital Dr. Lara Boyd, UBC Department of Physical Therapy Dr. Steven Brown, SFU Department of Psychology Dr. Kalina Christoff's Cognitive Neuroscience of Thought Laboratory Dr. Vince Di Lollo's Vision and Visual Attention Laboratory Dr. Janice Eng, UBC Department of Physical Therapy Dr. Deborah Giaschi's Visual Neuroscience Laboratory Dr. Todd Handy's Neuroimaging Lab Dr. Nicola Hodges' Motor Skills Laboratory Dr. Raymond Lam, Mood Disorders Centre of Excellence Dr. Mario Liotti's Laboratory for Affective and Developmental Neuroscience Dr. Teresa Liu-Ambrose, UBC Department of Physical Therapy Dr. Martin McKeown and Dr. Rafeef Abugharbieh's Biomedical Signal and Image Computing Laboratory Dr. Elton Ngan's Schizophrenia, Cognition and Imaging Laboratory Wayne Patola, St. Paul's Hospital Radiology Department Dr. Todd Woodward's Laboratory

fMRI Research Groups Outside Vancouver Functional Imaging Laboratory, University College London Oxford Centre for Functional Magnetic Resonance Imaging of the Brain Medical Research Council Cognition and Brain Sciences Unit Brain Mapping Unit, Department of Psychiatry, Cambridge Sir Peter Mansfield Magnetic Resonance Centre Brain Imaging Centre, Montreal Neurological Institute UCLA Brain Mapping Centre

UNIX and LINUX Simple Linux Tutorial by Alan Bates Unix System Administration Independent Learning Just Linux

Brain Atlases Harvard Whole Brain Atlas Digital Anatomist Project Useful neuroanatomy atlas for MRI work by Chris Rorden

MRI Safety MRISafety.com MR safety by Judith Behrens

General Statistics Statsoft Electronic Textbook Online SPSS Course by Lee Becker Page with many Stats links The R Project for Statistical Computing

Digital Signal Processing Online Digital Signal Processing Textbook ICA tutorial by Aapo Hyvarinen Wavelet Tutorial by Robi Polikar Books: Signal Processing for Neuroscientists: An Introduction to the Analysis of Physiological Signals, by van Drongelen

General Image Processing MRIcro and other resources by Chris Rorden Neuroimaging Informatics Technology Initiative (NIfTI) NIH Image ImageJ MRI artifact gallery by St. Paul's Hospital Radiology The little fMRI shop of horror (artifact indentification with ICA) fMRI Data Center Medical Image Samples by Sébastien Barré ScaleSpace by Mark Dow matplotlib (2D figure creation)

Imaging Societies Organization for Human Brain Mapping International Society for Magnetic Resonance in Medicine Society for Psychophysiological Research

Computer Port Information Good page for input and output port information PC connectivity information by Ian Harries

Commercial MRI Scanner Manufacturers Philips General Electric Bruker Siemens Toshiba Hitachi

Funding Agencies Canadian Institutes of Health Research Natural Sciences and Engineering Research Council of Canada Michael Smith Foundation for Health Research Canada Foundation for Innovation Science Council of British Columbia Vancouver Foundation Health Canada US National Institutes of Health US National Institute of Mental Health Human Frontier Science Program American Association for the Advancement of Science Grants and Funding Page

Journals Imaging Journals Neuroscience Journals Psychiatry Journals Psychology Journals Physiology Journals

Please address any questions or comments about this page to Alan Bates at bates (at) interchange.ubc.ca This page was originally created in June, 2005 at the UBC High Field MRI Centre while the author held a Health Professional Student Research Award from the Canadian Institutes of Health Research (CIHR). The page was updated in August, 2008 while the author was working as a resident in the St. Paul's Hospital Radiology Department.

UBC MRI Centre	Vancouver Hospital and Health Sciences Centre	Providence Health Radiology	University of British Columbia