Principles of FMRI data analysis

Below is an outline list of the areas of theory involved in functional imaging, and related documents that may help. Unfortunately some of these sources are difficult, but in my experience, all of them repay a slow reread, even if you think you understood almost nothing first time round. There is a bias towards SPM, but the same principles usually apply to other imaging packages.

General imaging introductions

• SliceTiming

• PrinciplesSpatialProcessing

• PrinciplesSmoothing

• PrinciplesStatistics

• PrinciplesMultipleComparisons

• PrinciplesRandomEffects

• LocatingActivation

• [wiki:Templates Templates]

• MniTalairach - differences between the MNI brain used by SPM and the Talairach atlas

• BrodmannAreas

• FindingCommissures

• AnatomyLinks

Useful background

• A very basic [http://imaging.mrc-cbu.cam.ac.uk/pdfs/matrices.pdf primer on matrices], in pdf format (see the [wiki:ReadingOnlineDocs online reading page] if you need help with pdf documents).

More specific SPM information

• SpmManuals

• The [http://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2/ Human Brain Function book] - these are a series of chapters covering theory and to some extent implementation in SPM of the areas below. Be warned that some of these chapters are aimed at quite a high level, and may be hard to follow for those without relevant background.

• [http://www.fil.ion.ucl.ac.uk/spm/dox.html Papers published by the FIL group on SPM] - these are available online via the SPM website, as are some other important papers on related theory.

• Rik Henson's SpmMiniCourse

Some of the links point to postscript documents, and some to Adobe Acrobat documents; for help on reading / printing these, see [wiki:ReadingOnlineDocs reading online documents].