These are files used to run Sequence Adaptive Multimodal Segmentation
(SAMSEG). See Puonti, Iglesias, Van Leemput, 2016. "Fast and
sequence-adaptive whole-brain segmentation using parametric Bayesian
modeling" Neuroimage. https://doi.org/10.1016/j.neuroimage.2016.09.011 

SAMSEG segments a brain image by maximizing the posterior probability
based on prior probability of a label being at a particular place and
an intensity likelihood based on a Gaussian mixture model (GMM); the
parameters of the GMM are determined from each image. The prior
probabilities are represented on a tetrahedral mesh. 

atlasForAffineRegistration.txt.gz - mesh that only has 5 labels:
Unknown, WM, GM, CSF, Skull. This is used for the initial affine
registration. This registration may fail if the input image does not
have extra cerebral-structures or only a single hemi.

atlas_level1.txt.gz, atlas_level2.txt.gz - these are meshes used to do
the actual segmentation.

sharedGMMParameters.txt - SAMSEG only runs the full optimization on a
small number of tissue types (eg, WM, GM, CSF, Skull, soft tissue,
background). Other structures (eg, hippocampus) are assigned to a
given superstructure. Each superstructure may be modeled by several
Gaussians. This file dictates which structures go into which
superstructure and how many Gaussians each superstructure gets. 

compressionLookupTable.txt - maps the labels numbers (eg, 0-43) to
FreeSurfer color table names and numbers. 

modifiedFreeSurferColorLUT.txt - FreeSurfer-style color table

template.nii - intensity image of the SAMSEG atlas. This is not
actually used in the normal course of SAMSEG execution, but it helpful
to have to evaluate registration.

template.seg.mgz - SAMSEG segmentation of the template.nii. This
more-or-less gives an indication of what the SAMSEG atlas priors look
like. This is not actually used in the normal course of SAMSEG
execution.

The files below are useful for ex vivo segmentation on samples that
only contain a hemisphere. There are two sets: (1) whole - samples
that include cerebellum and brainstem and (2) suptent - samples that
exclude those structures, ie, those that include only the
supratentorial region.  The template images are included so that the
initial affine registration can be run with mri_coreg because the
default SAMSEG registration often fails on these cases. These may be
deleted when the SAMSEG registration is improved.

exvivo.lh.whole.sharedGMMParameters.txt
exvivo.rh.whole.sharedGMMParameters.txt
exvivo.template.lh.whole.nii
exvivo.template.rh.whole.nii

exvivo.lh.suptent.sharedGMMParameters.txt
exvivo.rh.suptent.sharedGMMParameters.txt
exvivo.template.lh.suptent.nii
exvivo.template.rh.suptent.nii

