Introduction to fMRI
Introduction to fMRI
• Instructor: James Danckert
• Class times: Tuesdays 1:00 pm to 4:00 pm room PAS 4266
• Office Hours: Tuesdays and Thursdays 4:00 – 5:00 pm room 4040 PAS or
• Phone: extension 7014
• Email: email@example.com
Aims of the course
• To make you familiar with the different designs typically used in
fMRI research – e.g., block vs. event related and rapid event related
• To expose you to the most common analysis techniques of fMRI
including, t-tests, linear correlations, GLM, etc. To point you in the
right direction for more novel techniques not yet widely used such
• To briefly introduce you to alternate imaging techniques including
TMS, PET, EEG etc.
• To provide you with the practical skills to design, conduct and
analyze your own fMRI experiment.
• Each week’s reading will be in pdf format where possible and will be
available on the department web site
there follow the links to the course outline and the files will be easy
• The Powerpoint presentations for each class will be available on the
same website after each class
• For anything not available as a pdf I will make photocopies
Other recommended reading!
• John Ralston Saul Voltaire’s Bastards – this book has at least a
million messages, one of which is to avoid keeping secrets – in
other words, make sure you can communicate your results to
• Theodore Zeldin An Intimate History of Humanity – Zeldin shows
many different viewpoints on life exposing how people forget history
or ignore its influence on the present.
• Ramon y Cajal Advice for a Young Investigator – written in the
early part of last century this little book (much more so than the
other two!) has wisdom relevant to all of us – well worth reading.
• Critique the following fMRI paper and provide an alternate design that addresses
Marois, R., Chun, M.M., and Gore, J.C. Neural Correlates of the Attentional Blink.
Neuron, 28, 299 – 308.
Your paper should be less than 2000 words and counts for 30% of your mark.
• Design an fMRI study of your own. Present a brief (very brief!) theoretical
background, a detailed outline of design and analysis, justifying your choices.
Your paper should be less than 5000 words and counts for 40% of your mark.
• Class presentations – each student will give a 30 minute presentation on an fMRI
paper and will be expected to lead discussion on the issues raised. This will count
for 20% of your mark.
• Attendance and participation is worth the final 10% of your mark.
• Go to http://www.arts.uwaterloo.ca/~jdancker/fMRI/assess.htm for more details
Brain Voyager Seminar
• The software I use to analyze fMRI data is Brain Voyager –
although this software will be used throughout our discussions of
analysis techniques, the techniques themselves and the software
are largely independent of one another (with the exception of flat
mapping as we will see)
• After the class OR as part of it, we could arrange a two day seminar
on how to use the Brain Voyager software. This would be held at
the University of Western Ontario in the Goodale lab as they have
multiple licenses of the software suitable for group work.
• There may be a cost involved and of course you would have to
travel to London. So I would need to know as soon as possible the
number of people interested in doing such a course.