[[FreeSurferWiki|top]] | [[FileFormats|previous]]

== The GCA Subcortical Segmentation Atlas Volume Format ==

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:

 * [[attachment:gca.h]] 
 * [[attachment:gca.c]]
 * [[attachment:load_gca.m]]

The .gca file is composed of three volumes, which can be extracted like this:
{{{
mri_convert atlas.gca -nth 0 means.mgz
mri_convert atlas.gca -nth 1 labels.mgz
mri_convert atlas.gca -nth 2 priors.mgz
}}}

where:

 * means  --> the mean intensity of the most likely label
 * labels --> indices of the most likely label at each voxel (indices refer to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt)
 * priors --> the probability that that label occurs at that voxel

See also the script {{{rebuild_gca_atlas.csh}}} in the Freesurfer distribution for info on how the gca is built.

=== References ===
 * [[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.