References - aboualiaa/freesurfer GitHub Wiki

Surface Reconstruction

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

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

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

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

  • "A Hybrid Approach to the Skull-Stripping Problem in MRI", Ségonne, F., Dale, A.M., Busa, E., Glessner, M., Salvolini, U., Hahn, H.K., Fischl, B. (2004) NeuroImage, 22:1160-1075.

  • "Genetic Algorithm for the Topology Correction of Cortical Surfaces", F. Segonne, E. Grimson, B. Fischl (2005) IPMI pp393--405.

Inter-Subject Spherical Averaging

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

Thickness Measurement

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

  • "Reliability of MRI-derived measurements of human cerebral cortical thickness: The effects of field strength, scanner upgrade and manufacturer", Han et al. (2006) NeuroImage, 32(1):180-194.

Cortical Parcellation

  • "Automatically Parcellating the Human Cerebral Cortex", Fischl et al. (2004). Cerebral Cortex, 14:11-22.

  • "An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest", Desikan et al. (2006) NeuroImage 31(3):968-80.

  • "Atlas Renormalization for Improved Brain MR Image Segmentation Across Scanner Platforms", Han, X. and B. Fischl (2007) IEEE Transactions on Medical Imaging, 26(4):479-486.

Subcortical Segmentation

  • "Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain", Fischl et al. (2002) Neuron, 33:341-355.

  • "Sequence-Independent Segmentation of Magnetic Resonance Images", Fischl, B., Salat. D.H., van der Kouwe, A.J.W., Makris, N., Ségonne, F., and Dale, A.M. (2004) NeuroImage 23:S69-S84.

Related Methodological Papers

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

  • "Permutation Tests for Classification: Towards Statistical Significance in Image-Based Studies", P. Golland and B. Fischl (2003) Proc. IPMI2003: 18th International Conference on Information Processing in Medical Imaging.

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