Neuroscience:Functional MRI

These notes are based on the examination of various syllabi available on the web to enhance the research at The Cromwell Workshop. For example, Professor Marty Sereno has a good syllabus for his cognitive science 276 class on Neuroimaging at (http://www.cogsci.ucsd.edu/~sereno/276/) with plenty of references, readings and links to the field of neuroimaging-MRI, fMRI, EEG and MEG.

Another good example is Professor Calhoon's Analyis Methods in fMRI at(http://www.ece.unm.edu/~vcalhoun/courses/fMRI_Spring07/Syllabus.pdf) with texts and readings. One of the articles that I particularly like is at

http://afni.nimh.nih.gov/sscc/staff/rwcox/ISMRM_2006/Syllabus%202006%20-%203340/files/J_06.pdf

which uses Independent component analysis (ICA) for feature set detection. The use of Bayesian techniques and state space models in this context should prove useful for some of the observations made in the conclusion of the paper.

Another good interdisciplinary course is from the group of professors Hernandez, Jonides, Nichols and Noll at the University of Michigan.

http://www.umich.edu/~fmri/course/2005/ . Dr. Noll has a very good primer on MRI and fMRI at http://www.umich.edu/~fmri/course/2005/primer2.pdf as well as their lab exercies in MatLab.

If you go through these course, readings and labs, you will have a good foundation to be able to diagnose potential problems in the field and how different spatial-temporal models can be used to solve them. Of course, good papers that should be read on fMRI time series analysis from both the frequency and Bayesian perspectives are:

(1) http://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2/pdfs/Ch10.pdf
(2) http://www.fil.ion.ucl.ac.uk/~wpenny/publications/vb2_2005.pdf

and the deconvolution of fMRI time series data can be found at

http://www.cogsci.ucsd.edu/~sereno/276/readings/3dDeconvolve.pdf

Journals for fMRI research are:

• NeuroImage http://www.sciencedirect.com/science/journal/10538119
• Neurocomputing http://www.sciencedirect.com/science/journal/09252312
• Journal of Magnetic Resonance Imaging http://www3.interscience.wiley.com/cgi-bin/jhome/10005199
• Magnetic Resonance Imaging http://www.sciencedirect.com/science/journal/0730725X

Yale has some interesting software for fMRI that uses MATLAB code by Pawel Skudlarski at (http://mri.med.yale.edu/individual/pawel/fMRIpackage.html). Statistical parameteric mapping software can be obtained at (http://www.fil.ion.ucl.ac.uk/spm/software/).

Of course, this is a topic for another post.