Principles of FMRI data analysis

The aim of these pages is to introduce the theory behind different processing stages. If you're interested in the practicalities of how to do an analysis, you might want the [:AnalysisSoftware:software] page instead.

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

Pre-processing

• [:SliceTiming:Slice timing] - correcting for the fact that different slices in the brain are acquired at different times

• PrinciplesSpatialProcessing

• PrinciplesSmoothing

Statistics

• PrinciplesStatistics

• PrinciplesMultipleComparisons

• PrinciplesRandomEffects

More advanced issues

• DealingWithDifference - HRF responses can differ from area to area

• [wiki:Templates Templates]

• LocatingActivation

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

• BrodmannAreas

• FindingCommissures

• AnatomyLinks

Introductions to the theory and algorithms behind SPM

Presentations

• CBU SpmMiniCourse2007

• Rik Henson's SpmMiniCourse2008

Written guides

• [http://www.fil.ion.ucl.ac.uk/spm/ FIL/SPM home page]

• SpmQuickStart

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).