Descritiption and Aims: The course aims to introduce students to the brain imaging technique of functional magnetic resonance imaging (fMRI). Students will be given an overview of the physics involved in this technique, as well as some comparison with other brain imaging techniques (VEPs, TMS, PET etc.). The course will focus primarily on issues of design and analysis of fMRI experiments. Block and single-event designs will be introduced and various statistical methods for analysing fMRI data will be explored. No set text will be assigned to this course. Instead, specific articles relating to each issue will be placed on the Department web site in pdf format. If you have trouble reading pdf files please contact me and we can make other arrangements.
Course Requirements:
Assessment: Students will be required to make a 30 minute presentation in class discussing a pertinent article (set by Instructor). This presentation will form 20% of the final mark. Students will then be asked to submit two written assignments. The first will be a 2000 word critique of an fMRI paper (a standard paper will be allocated for this purpose) which will constitute 30% of the final mark and the second will be a 5000 word proposal for an fMRI experiment. This will constitute the 40% of the final mark. Class participation and attendance will constitute the remaining 10% of the final mark. Detailed outlines of the written assignments will be distributed in class. click here for further information
Reading material: Reading material for each week is outline below. In general, articles will be in pdf format (you can download Adobe Acrobat Reader for free from http://www.adobe.com/products/acrobat/readstep2.html if you don't already have it) and will be posted on the Department website at http://www.psychology.uwaterloo.ca/people/jdancker/ - follow the links to fMRI course materials). Where an article is not available in pdf I will make photocopies and post them on my door.
Student Information: Information for students only via a separate website to be emailed to the group.
Course Timetable: 1.5 to 3 hours every week Tuesdays 1:00 pm
start in room PAS 4266.
This will give us a chance to discuss the aims of the course, previous experience with functional imaging techniques and to assign papers for presentation to each student taking the course for credit.
Reading:
Fox, P. (1997) The growth of human brain mapping. Human Brain Mapping, 5, 1 - 2. (pdf)
Powerpoint file: Introduction.ppt
A broad introduction to the structure and functions of the major brain regions in humans. Focus will be on surface cortical structures and blood supply. This will be invaluable to orient you to what comes later. I will then give a very broad brush stroke of fMRI - this will at least put the physics that follows in some context.
Reading:
Savoy, R. (2001) History and future directions of human brain mapping and functional neuroimaging. Acta Psychologia, 107, 9 - 42. (pdf) (Student Presentation 1)
Powerpoint file: Neuroanatomy.ppt and The Basic Story.ppt
************************************************************************
No classes for the week Tuesday 24th of September - I will be in the UK for a conference.
************************************************************************
I do not claim to have an in depth knowledge of the fundamental physics involved in fMRI. What this week will aim to do is to give you an introduction to the what and how of fMRI. For those interested in more detailed descriptions of this important part of fMRI, further resources will be available.
Reading:
D. C. Noll (2001) A Primer on MRI and Functional MRI (pdf)
Extra Reading:
Cox, R. (in preparation) Ch 2. The Physics of Magnetic Resonance Imaging. (word document)
Cohen, M.S. and Bookheimer, S.Y. Functional Magnetic Resonance Imaging. (word document)
Powerpoint file: fMRI Physics.ppt and Measuring the BOLD response.ppt
This will be the final didactic lecture in the course and aims to introduce you to the principal factors affecting SNR in fMRI research and to discuss the possible solutions and trade offs of those solutions (fMRI is all about maximizing the SNR and this always means trade-offs!).
Powerpoint file: SNR and Data Quality.ppt
No readings.
This will give you an introduction to the most common experimental design in
functional imaging (true for PET as well as fMRI).
Student presentations: 2
Reading:
Gruber SA, et al. (2002) Stroop performance in normal control subjects: An
fMRI study. NeuroImage, 16, 349-360. (pdf) (Student presentation
1)
Kanwisher et al. (1997) The fusiform face area: a module in human extrastriate
cortex specialized for face perception. The Journal of Neuroscience, 17, 4302-4311.
(pdf) (Student presentation 2)
Extra reading:
van Veen et al. (2001) Anterior cingulated cortex, conflict monitoring, and
levels of processing. NeuroImage, 14, 1302-1308. (pdf) (related to Student presentation
1 - event-related design)
Gauthier I., et al. (1999) Activation of the middle fusiform 'face area' increases
with expertise in recognizing novel objects. Nature Neuroscience, 2, 568-573.
(pdf) (related to Student presentation 2)
Powerpoint file: fMRI basic design issues.ppt
We will discuss the different kinds of event-related (single event-related and rapid event-related) fMRI designs. Again, this will be about the trade-offs!
Student presentations: 2
Reading:
Bandettini, P.A. and Cox, R.W. (2000) Event-related fMRI contrast when using constant interstimulus interval: theory and experiment. Magnetic Resonance in Medicine, 43, 540 - 548. (pdf) (Student Presentation 1)
Maccotta, L., et al. (2001) Rapid self-paced event-related functional MRI:
feasibility and implications of stimulus- versus response-locked timing. NeuroImage,
14, 1105 - 1121. (pdf) (Student Presentation2)
Extra reading:
Dale, A.M. & Buckner, R.L. (1997) Selective averaging of rapidly presented individual trials using fMRI. Human Brain Mapping, 5, 329 - 340. (pdf)
Josephs, O., et al. (1997) Event-related fMRI. Human Brain Mapping, 5, 243 - 248. (pdf)
Price, C.J., et al. (1999) The critical relationship between the timing of stimulus presentation and data acquisition in blocked designs with fMRI. Neuroimage, 10, 36 - 44. (pdf)
Ollinger, J.M. et al. (2001) Separating processes within a trial in event-related functional MRI. I. The method. NeuroImage, 13, 210 - 217. (pdf)
Ollinger, J.M. et al. (2001) Separating processes within a trial in event-related functional MRI. II. Analysis. NeuroImage, 13, 218 - 229. (pdf)
Hinrichs, H., et al. (2000) Deconvolution of event-related fMRI responses in fast-rate experimental designs: tracking amplitude variations. Journal of Cognitive Neuroscience, 12, 76 - 89. (pdf)
Powerpoint file: event related fMRI design issues.ppt
The most basic analyses used in fMRI (and in PET) studies involve t-tests and
linear correlations to determine whether activation is linked to the protocol
used. These techniques are outlined here.
Student presentations: 2
Reading:
Buxton Statistical Analysis of BOLD data. CH 18 in Introduction to functional magnetic resonance imaging: principles and techniques. (photocopy) - this is relevant for the next two weeks.
t-tests: de Fockert JW., et al. (2001) The role of working memory in visual selective attention. Science, 291, 1803-1806. (pdf) (Student presentation 1)
correlations: Brefczynski and De Yoe (1999) A physiological correlate of the 'spotlight' of attention. Nature Neuroscience, 2, 370 - 374. (pdf) (Student presentation 2)
Extra reading:
Martinez, A., et al. (1999) Involvement of striate and extrastriate visual cortical areas in spatial attention. Nature Neuroscience, 2, 364 - 369. (pdf) Relevant for correlational analysis.
Powerpoint file: fMRI analysis_t-tests_vs_correlations.ppt
With more factors (predictors) and greater interweaving of conditions within a scanning run more complicated analyses are required. The GLM (which is largely an ANOVA) can address this issue. We may also touch briefly on Independent Components Analysis (ICA).
Student presentations: 2
Reading: refer again to Buxton Ch 18.
Palmer et al. (2001) An event-related fMRI study of overt and covert word stem completion. NeuroImage, 14, 182-193. (pdf) (Student presentation 1)
Calhoun et al. (2001) fMRI activation in a visual-perception task: network of areas detected using the general linear model and independent components analysis. NeuroImage, 14, 1080-1088. (pdf) (Student presentation 2)
Powerpoint file: fMRI analysis_GLM.ppt
Perhaps the two most important aspects of design in fMRI studies are the use of good baseline conditions and the appropriate choice of contrast conditions (these are obviously related but not the same!). Issues concerning these elements of fMRI design will be discussed here.
Student presentations: 2
Reading:
Stark CEL and Squire LR. (2001) When zero is not zero: the problem of ambiguous baseline conditions in fMRI. PNAS, 98, 12760 - 12766. (pdf) (Student presentation 1)
Culham J., et al. (in preparation) fMRI reveals a dissociation between object grasping and object recognition. (Culham.doc, Fig. 1-3, Fig. 4, Fig. 5) (Student presentation 2)
Powerpoint file: Baselines and contrasts.ppt
After all of this, are we really measuring what we say we're measuring? And how do we know? These are complicated issues but with some intriguing new answers.
Student presentations: 2
Reading:
Logothetis, N., et al. (2001) Neurophysiological investigation of the basis of the fMRI signal. Nature, 412, 150 - 157. (pdf) (Student Presentation 1)
Authurs, O.J. and Boneface, S. (2002) How well do we understand the neural origins of the fMRI BOLD signal? TRENDS in Neuroscience, 25, 27 - 31. (pdf) (Student presentation 2)
Extra Reading:
Bandettini, P.A., and Ungerleider, L.G. (2001) From neuron to BOLD: new connections. Nature Neuroscience, 4, 864 - 866. (pdf)
Raichle, M.E. (2001) Bold insights. Nature, 412, 128 - 130. (pdf)
Brewer JB and Moghekar A. (2002) Imaging the medial temporal lobe: exploring new dimensions. TICS, 6, 217-223. (pdf)
Martinez A. et al. (2001) Putting spatial attention on the map: timing and localization of stimulus selection processes in striate and extrastriate visual areas. Vision Research, 41, 1437-1457. (pdf)
One could be excused for thinking fMRI is God's gift to Cognitive Neuroscience!
But despite its rise in popularity there are alternatives to understanding brain
function. Some of the major ones will be discussed this week with a focus on
pros and cons.
Student presentations: 2
Reading:
Devlin, J.T. et al (in press) Susceptibility induced loss of signal: comparing PET and fMRI on a semantic task. (pdf) (Student Presentation 1)
Paus, T. (1999) Imaging the brain before, during and after transcranial magnetic stimulation. Neuropsychologia, 37, 219 - 224. (pdf) (Student presentation 2)
Extra Reading: I recommend you re-read the Savoy article from Week 2.
Powerpoint file: Alternate imaging techniques.ppt
We haven't touched on flat-mapping. The issue of co-registration either of
different brains or of the same brains across different sessions represents
a major problem for fMRI studies. Flat mapping and inflated maps (as well as
making the brain the world!) represents one way in which this issue can be addressed.
Reading:
Fischl, B. et al. (1999) High-resolution intersubject averaging and a co-ordinate system for the cortical surface. Human Brain Mapping, 8, 272 - 284. (pdf) (Presentation)
Powerpoint file: Flat mapping and subject averaging.ppt