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* [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain], Fischl, B., D.H. Salat, E. Busa, M. Albert, M. Dieterich, C. Haselgrove, A. van der Kouwe, R. Killiany, D. Kennedy, S. Klaveness, A. Montillo, N. Makris, B. Rosen, and A.M. Dale, (2002). Neuron, 33:341-355. * [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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. * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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. |
* [[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf|Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain]], Fischl, B., D.H. Salat, E. Busa, M. Albert, M. Dieterich, C. Haselgrove, A. van der Kouwe, R. Killiany, D. Kennedy, S. Klaveness, A. Montillo, N. Makris, B. Rosen, and A.M. Dale, (2002). Neuron, 33:341-355. * [[http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf|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. * [[https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf|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. |
The GCA Subcortical Segmentation Atlas Volume Format
WORK IN PROGRESS
The .gca (Gaussian Classifier Atlas) file format encodes voxel label information based on probabilistic information estimated from a training set. The GCA format is proprietary, defined by the NMR Center (at Massachusetts General Hospital). Below is an informal specification of the format, extracted from the code snippets below:
References
Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl, B., D.H. Salat, E. Busa, M. Albert, M. Dieterich, C. Haselgrove, A. van der Kouwe, R. Killiany, D. Kennedy, S. Klaveness, A. Montillo, N. Makris, B. Rosen, and A.M. Dale, (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.
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.