There are numerous sources of artifact in functional imaging data.

• Sources of image artifacts
• Detecting artifacts
• Artifact mitigation
• Using the Art tools to detect and mitigate the effects of artifacts

The ART tools can be downloaded here.
 
Quality Assurance Lecture
 
References
Johnstone T,Ores K.S., Walsh O, Greischar LL, Alexander AL, Fox AS, Davidson RJ, Oakes TR (2006) Motion correction and the use of motion covariates in multiple-subject fMRI analysis. Human Brain Mapping 27:779-788
Bullmore ET, Brammer MJ, Rabe-Hesketh S, Curtis VA, Morris RG, Williams SCR., Sharma T, McGuire PK (1998) Methods for diagnosis and treatment of stimulus-correlated motion in generic brain activation studies using fMRI. Human Brain Mapping 7: 38-48
Jezzard P and Balaban RS (1995) Correction for geometric distortions in echoplanar images from B0 field variations. Magn Reson Med 34:65-73
Andersson JLR, Hutton C, Ashburner J, Turner R, Friston K (2001) Modelling geometric deformations in EPI time series. NeuroImage 13:903-919
Hutton C, Bork A, Josephs O, Deichmann R, Ashburner J, Turner R. (2002). Image distortion correction in fMRI: A quantitative evaluation. NeuroImage 16:217-240
Jenkinson M. (2003). Fast, automated, N-dimensional phase-unwrapping algorithm. MRM 49:193-197
Hutton, C., Deichmann, R., Turner R., Andersson, J. L. R., (2004). Combined correction for geometric distortion and its interaction with head motion in fMRI. Proceedings of ISMRM 12, Kyoto, Japan