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Applied Neuroimaging fMRI Mini-Course

University of Warwick fMRI Reading Group

The reading group is now on hiatus with the end of the term and summer break. We will re-commence with the fall term, 7th of October, 2010. Please contact Tom Nichols if you have idea for speakers and/or papers to discuss, or need consultation on fMRI studies until then.

2010 Schedule, Spring & Summer Terms - Now finished
2-3pm Thursdays, Room A1.01 Zeeman Building (Math & Statistics)

Directions to meeting location: Upon entering the Zeeman building, turn immediately to your right, entering the stairwell and going up one flight; on leaving the stairwell A1.01 is to your immediate left.

Except for monthly fMRI didactic lectures, this is a standard journal club were participants present papers of interest related to fMRI research; structural MRI and other related topics are also welcome topics.

If you plan on attending at all, please be sure to sign up for the fMRI reading group email list here. The email list will be used to give last minute updates to the schedule, e.g. cancellations, and should have minimal traffic otherwise.

Coordinators: Tom Nichols, Matthew Broome, Gemma Calvert




14 Jan

MR Physics - physiological basis of BOLD
Reading: A Primer on MRI and Functional MRI, Doug Noll.
Additional reading: Less detail, a little more detail (see Ch 1-5), and lots more technical detail.
Slides: FSL Course Intro

Tom N

21 Jan



28 Jan

Spatial Preprocessing
Slides: FSL Lecture Notes (starting from page 9 of these 4-up notes)
Additional Material: Section III of the SPM introduction has a very short summary
Chapters 2-6 of the SPM Book have extensive details on the corresponding pre-processing steps

Tom Nichols

4 Feb

fMRI of Psychopathology
Reading: "Functional brain mapping of psychopathology", Honey et al, J Neurol Neurosurg Psychiatry 2002;72:432-439.
Additional reading: "Functional neuroimaging in schizophrenia: diagnosis and drug discovery", McGuire et al, Trends in Pharmacological Sciences Vol.29 No.2.

Additional references:
"Regionally Localized Thinning of the Cerebral Cortex in Schizophrenia", Kuperberg, et al, Arch Gen Psychiatry. 2003;60:878-888
"Functional integration between the posterior hippocampus and prefrontal cortex is impaired in both first episode schizophrenia and the at risk mental state", Benetti et al, Brain, doi:10.1093/brain/awp098.

Matthew B

11 Feb

Reading: "Neural Predictors of Purchases", Knutson et al, Neuron 53, 147-156, January 4, 2007

Additional Reading:
Hedgecock & Rao, "Trade-Off Aversion as an Explanation for the Attraction Effect: A Functional Magnetic Resonance Imaging Study", J Marketing Research, 46(1), 2009: Main Paper Commentaries & Rejoinder

Zhuohao Chen

18 Feb

< canceled >


25 Feb

GLM Intro - Modelling BOLD Response

Slides: FSL Lecture Notes
Additional Material: Section IV-A of the SPM introduction has a very short summary
Chapters 10 & 11 of the SPM Book have extensive details on BOLD modelling

Tom N

4 Mar

Crossmodal Processing in the Human Brain
Reading: "Crossmodal Processing in the Human Brain: Insights from Functional Neuroimaging Studies", Calvert, Cerebral Cortex, 11:1110-1123, 2001

Gemma C

11 Mar

Brain imaging of conscious and nonconscious cognitive control: Paradigms and problems
Reading: Imaging unconscious semantic priming, Nature 395:597-600, 1998.
Additional Reading: Inhibition of subliminally primed responses is mediated by the caudate and thalamus: evidence from functional MRI and Huntington's disease, Brain 126:713-723, 2003.

Friederike Schlaghecken & Paolo Martini

18 Mar

Inference on Images
Slides: Thresholding
Additional Reading: Corresponding (but much less detailed) FSL course slides;
Section IV-B of the SPM introduction has a very short summary;
Chapter 14 of the SPM Book has a gentle introduction to Random Field Theory, while Chapter 15 has a more mathematical overview; Chapter 16 covers permutation inference.

Tom N

25 Mar

(break - no meeting)


1 Apr

(break - no meeting)


8 Apr

(break - no meeting)


15 Apr

(break - no meeting)


22 Apr

(break - no meeting)


29 Apr

Experimental Design
The excellent Design Efficiency website by Rik Henson.
Similar, but in a more traditional format is Henson's Chapter 10 of the SPM Book, giving great detail on the analysis and modelling of block and event-reated fMRI data.

Tom N

6 May

(No meeting)


12 May

(No meeting)


20 May

Group Analysis & Mixed effects
Reading: While quite detailed, I find Penny & Holmes' Chapter 15 of the SPM Book is a great reference.
Slides: Nichols_GroupStats.pdf

Tom N

27 May

Reliability in MRI and fMRI
Reading: Bennett & Miller. (2010). How reliable are the results from functional magnetic resonance imaging? Annals of the New York Academy of Sciences, 1191, 133-155.
Jovicich, Czanner, Greve, Haley, Kouwe, et al. (2006). Reliability in multi-site structural MRI studies: effects of gradient non-linearity correction on phantom and human data. Neuroimage, 30, 436-443.
Han, Jovicich, Salat, van der Kouwe, Quinn, Czanner, et al. (2006). Reliability of MRI-derived measurements of human cerebral cortical thickness: the effects of field strength, scanner upgrade and manufacturer. NeuroImage, 32(1), 180-94.
Jovicich, Czanner, Han, Salat, van der Kouwe, Quinn, et al. (2009). MRI-derived measurements of human subcortical, ventricular and intracranial brain volumes: Reliability effects of scan sessions, acquisition sequences, data analyses, scanner upgrade, scanner vendors and field strengths. NeuroImage, 46(1), 177-92.

Silvester Czanner

3 Jun

Fabio Rigat & George Minas on Adaptive Experimental Design for fMRI

Matthew B

10 Jun

None (OHBM)


17 Jun

Human-Brain Interfaces

Reading: Assessing NeuroSky’s Usability to Detect Attention Levels in an Assessment Exercise, Rebolledo-Mendez et al, HCI international 2009, in press.

Ian Dunwell, Serious Games Institute

24 Jun