Principles of 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 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.
Introduction to imaging
Check for CommonArtefacts
If you are unfortunate enough to find bad data, consider whether to RemoveBadScans
Typical pre-processing stages
These are the stages typical to most analyses
Slice timing - correcting for the fact that different slices in the brain are acquired at different times
Undistort EPIs using field maps - usually no longer necessary on data from the Siemens scanner
Motion correction - correcting for subject movement through an fMRI scan, sometimes called realignment
Introductions to the theory and algorithms behind SPM
The 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.
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.
More advanced issues
ParametricModulations - and the issue of orthogonalisation
DealingWithDifference - HRF responses can differ from area to area
MniTalairach - differences between the MNI brain used by SPM and the Talairach atlas
This is a systematic and well-illustrated introduction to linux.
For Matlab, you can look at tutorials and demos offered by Mathworks itself. This site also contains links to Matlab tutorials at some universities. You may want to start with the Getting Started section. The short introduction to Matlab for psychologists from the University of Nottingham is also useful.
Look here for more information on software.