if you use surface recons:

Dale, A.M. and M.I. Sereno (1993) Improved localization of cortical activity by combining EEG and MEG with MRI cortical surface reconstruction: A linear approach. Journal of Cognitive Neuroscience 5:162-176. pdf

Segonne F, Dale, AM, Busa E, Glessner M, Salvolini U, Hahn HK, Fischl B, A Hybrid Approach to the Skull-Stripping Problem in MRI. NeuroImage, 22, pp. 1160-1075, 2004 pdf

Dale, A.M., Fischl, Bruce, Sereno, M.I., (1999). Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction. NeuroImage 9(2):179-194 pdf

Fischl, Bruce, Sereno, M.I., Dale, A.M., (1999). Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System. NeuroImage 9(2):195-207 pdf

Fischl, Bruce, Liu, Arthur, and Dale, A.M., (2001). Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex. IEEE Transactions on Medical Imaging, 20(1):70-80 pdf

F. Segonne, E. Grimson, B. Fischl, Genetic Algorithm for the Topology Correction of Cortical Surfaces, IPMI 2005, pp.393--405. pdf

if you do inter-subject spherical averaging:

Fischl, Bruce, Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). High-resolution inter-subject averaging and a coordinate system for the cortical surface. Human Brain Mapping, 8:272-284 pdf

if you do a thickness study:

Fischl, Bruce, and Dale, A.M., (2000). Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Images. Proceedings of the National Academy of Sciences, 97:11044-11049. pdf

Xiao Han, Jorge Jovicich, David Salat,Andre van der Kouwe, Brian Quinn, Silvester Czanner, Evelina Busa, Jenni Pacheco, Marilyn Albert, Ronald Killiany, Paul Maguire, Diana Rosas, Nikos Makris, Anders Dale, Bradford Dickerson, and Bruce Fischl, (2006). Reliability of MRI-derived measurements of human cerebral cortical thickness: The effects of field strength, scanner upgrade and manufacturer. NeuroImage, 32(1):180-194. pdf

also, Rosas et al (histology) and Kuperberg (MRI) were validation studies for the thickness measures.

if you use cortical parcellations:

Fischl B, van der Kouwe A, Destrieux C, Halgren E, Ségonne F, Salat DH, Busa E, Seidman LJ, Goldstein J, Kennedy D, Caviness V, Makris N, Rosen B, Dale, AM Automatically Parcellating the Human Cerebral Cortex. Cerebral Cortex, 2004; 14:11-22. pdf

Desikan RS, Segonne F, Fischl B, Quinn BT, Dickerson BC, Blacker D, Buckner RL, Dale AM, Maguire RP, Hyman BT, Albert MS, Killiany RJ (2006). An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Neuroimage. 31(3):968-980 pdf

if you do subcortical segmentation:

Fischl B, Salat DH, van der Kouwe AJW, Makris N, Ségonne F, Dale AM. Sequence-Independent Segmentation of Magnetic Resonance Images. NeuroImage 2004, 23 Suppl 1, S69-84. pdf

Fischl B, Salat D, Busa E, Albert M, Dieterich M, Haselgrove C, van der Kouwe A, Killiany R, Kennedy D, Klaveness S, Montillo A, Makris N, Rosen B, Dale A.M.. Whole brain segmentation. Automated labeling of neuroanatomical structures in the human brain. Neuron. 2002; 33(3): 341-355. pdf

other methodological papers:

P. Golland, B. Fischl, M. Spiridon, N. Kanwisher, R.L. Buckner, M.E. Shenton, R. Kikinis, A. Dale, W.E.L. Grimson. Discriminative Analysis for Image-Based Studies. In Proc. MICCAI'2002: Fifth International Conference on Medical Image Computing And Computer Assisted Intervention. LNCS 2488:508-515, 2002. pdf

P. Golland and B. Fischl. Permutation Tests for Classification: Towards Statistical Significance in Image-Based Studies. To Appear in Proc.~IPMI'2003: 18th International Conference on Information Processing in Medical Imaging, July 2003. pdf

F. Segonne, E. Grimson and B. Fischl (2003). Topology Correction of Subcortical Segmentation", MICCAI 2003. pdf

Salat, D., R. Buckner, A. Snyder, D. Greve, R. Desikan, E. Busa, J. Morris, D. AM, and B. Fischl, Thinning of the cerebral cortex in aging. Cerebral Cortex, 2004. 14: p. 721-730. pdf

misc other ones:

Jean C. Augustinack, Andre J. W. van der Kouwe, Megan L. Blackwell, David H. Salat, Christopher J. Wiggins, Matthew P. Frosch, Graham C. Wiggins, Andreas Potthast, Lawrence L. Wald, Bruce R. Fischl (2005). Detection of entorhinal layer II using 7 Tesla magnetic resonance imaging. Annals of Neurology, 57(4):489-494. pdf

Rauch, S., C. Wright, B. Martis, E. Busa, K. McMullin, L. Shin, A. Dale, and B. Fischl, A magnetic resonance imaging study of cortical thickness in animal phobia. Biological Psychiatry, 2004. 55(9): p. 946-952. pdf

Rosas, H.D., A.K. Liu, S. Hersch, M. Glessner, R.J. Ferrante, D.H. Salat, A. van der Kouwe, B.G. Jenkins, A.M. Dale, and B. Fischl, Regional and progressive thinning of the cortical ribbon in Huntington's disease. Neurology, 2002. 58(5): p. 695-701. pdf

Kuperberg, G., M. Broome, P. McGuire, A. David, M. Eddy, F. Ozawa, D. Goff, W. West, S. Williams, A. van der Kouwe, D. Salat, D. AM, and B. Fischl, Regionally localized thinning of the cerebral cortex in schizophrenia. Archives of General Psychiatry, 2003. 60: p. 878-888. pdf

Sailer, M., B. Fischl, D. Salat, C. Tempelmann, M. Schonfeld, E. Busa, N. Bodammer, H. Heinze, and A. Dale, Focal thinning of the cerebral cortex in multiple sclerosis. Brain, 2003. 126(9): p. 1734-1744. pdf

Gold, B.T., D.A. Balota, M.J. Cortes, S.D. Sergent-Marshall, A.Z. Snyder, D.H. Salat, B. Fischl, A.M. Dale, J.C. Morris, and R.L. Buckner, Differing neuropsychological and neuroanatomical correlates of abnormal reading in early-stage semantic dementia and dementia of the Alzheimer type. Neuropsychologia, 2005. 43: p. 833-846. pdf

Fjell, A.M., K.B. Walhovd, I. Reinvang, A. Lundervold, A.M. Dale, B.T. Quinn, N. Makris, and B. Fischl, Age does not increase rate of forgetting over weeks neuroanatomical volumes and visual memory across the adult life-span. Journal of the International Neuropsychological Society, 2005. 2-15(1): p. 2-15.

Walhovd, K.B., A.M. Fjell, I. Reinvang, A. Lundervold, B. Fischl, B.T. Quinn, N. Makris, and A.M. Dale, Cortical volume and speed-of-processing are complementary in prediction of performance intelligence. Neuropsychologia, 2005. 43(5): p. 704:13.