eanatSelect: Selection of n eigenvectors and sparsity for eigenanatomy

In neuroconductor-devel/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

Description

The algorithm automatically selects the key nvecs and hidden sparseness parameters. The user should select the cthresh regularization parameters for his or her application. The principle used here is that we want few but sparse pseudo-eigenvectors that are minimally correlated in row-space. true left and right eigenvectors are uncorrelated in both row and column (left and right eigenvector) spaces, but this is not the case when we impose sparsity.

Usage

eanatSelect(
  inmat,
  mask = NULL,
  cthresh = 0,
  smooth = 0,
  maxNEvec = 0,
  selectorScale = 1.1,
  whiten = FALSE,
  verbose = FALSE
)

Arguments

inmat	input matrix
mask	input mask, must match matrix
cthresh	remove isolated voxel islands of size below this value
smooth	smooth the input data first by this value
maxNEvec	integer that, if set greater than zero, indicates that we use a low-rank approximation to the input matrix before proceeding to eanat. this value should be greater than nvecs
selectorScale	influences automatic selection of nvecs and tries to find the knee in the correlation plot. This parameter produces fewer, less sparse eigenanatomy pseudo-eigenvectors as its value increases. Its minimum value is 1 and a reasonable range is between 1 and 2. The user should look at the plot produced when verbosity is turned on.
whiten	use ICA style whitening.
verbose	controls whether computation is silent or not.

Value

nvecs is output, analogous to nvecs in svd(mat,nu=0,nv=nvecs)

Author(s)

Avants BB, Tustison NJ

Examples

## Not run: 
mat <- matrix(rnorm(2000),ncol=50)
nvecsSel<-eanatSelect( mat, selectorScale = 1.2, maxNEvec = 4 )
esol <- sparseDecom( mat, nvecs = nvecsSel )
print(paste("selected", nvecsSel,'pseudo-eigenvectors'))

## End(Not run)

neuroconductor-devel/ANTsR documentation built on April 1, 2021, 1:02 p.m.