extract-methods: Methods for Function 'extract' and '[' in Package 'dti'
In neuroconductor/dti: Analysis of Diffusion Weighted Imaging (DWI) Data

Description Usage Arguments Value Methods Author(s) See Also

The methods extract and/or compute specified statistics from object of class "dtiData", "dtiTensor", and "dtiIndices". This can be restricted to a subset of voxel.

  ## S4 method for signature 'dtiData'
extract(x,
    what=c("data","gradient","btb","s0","sb","siq"),
    xind=TRUE, yind=TRUE, zind=TRUE)
  ## S4 method for signature 'dtiTensor'
extract(x, what=c("tensor", "fa", "ga", "md", "evalues",
      "andir", "s0", "mask", "bic", "aic", "outlier"),
    xind=TRUE, yind=TRUE, zind=TRUE, mc.cores = setCores(, reprt = FALSE))
  ## S4 method for signature 'dwiMixtensor'
extract(x, what=c("w0","andir", "order", "ev", "mix", "s0",
      "mask", "fa", "eorder", "bic", "aic"), xind=TRUE, yind=TRUE, zind=TRUE)
  ## S4 method for signature 'dtiIndices'
extract(x, what=c("fa", "andir", "ga", "md", "bary"),
    xind=TRUE, yind=TRUE, zind=TRUE)
  ## S4 method for signature 'dwiQball'
extract(x, what=c("sphcoef", "s0", "mask", "bic", "aic",
      "outlier"), xind=TRUE, yind=TRUE, zind=TRUE)
  ## S4 method for signature 'dtiData'
x[i, j, k, drop=FALSE]
  ## S4 method for signature 'dtiTensor'
x[i, j, k, drop=FALSE]
  ## S4 method for signature 'dtiIndices'
x[i, j, k, drop=FALSE]
  ## S4 method for signature 'dkiTensor'
x[i, j, k, drop=FALSE]
  ## S4 method for signature 'dkiIndices'
x[i, j, k, drop=FALSE]
  ## S4 method for signature 'dwiQball'
x[i, j, k, drop=FALSE]

`x`	Object of class `dti`
`i`	vector of x-coordinates, defaults to whole range.
`j`	vector of y-coordinates, defaults to whole range.
`k`	vector of z-coordinates, defaults to whole range.
`xind`	vector of x-coordinates, defaults to whole range.
`yind`	vector of y-coordinates, defaults to whole range.
`zind`	vector of z-coordinates, defaults to whole range.
`what`	Statistic to extract. See Methods Section for details.
`drop`	unused.
`mc.cores`	Number of cores to use. Defaults to number of threads specified for openMP, see documentation of package awsMethods. Our experience suggests to use 4-6 cores if available.

For function extract a list with components carrying the names of the options specified in argument what. For code"[" the cutted object.

The generic extract function "[" does what it is expected to do: it extracts parts of the object specified by i, j, and k.

x = "ANY": Returns a warning for extract. Generic funtion for "[" returns an object of same class with data clipped to the indices specified in arguments i, j and k.
x = "dtiData": Extraction of squared gradient matrix "btb" or of S0 "s0", Sb "sb", Si/mean(SO) "siq" or all images "data" restricted to the cube defined by arguments i, j and k.
x = "dtiIndices": Returns an array containing the specified statistics, i.e. fractional anisotropy "fa", geodesic anisotropy "ga", mean diffusivity "md", main direction of anisotropy "andir" and/or shape parameters "bary", as specified in argument what. Information is extracted for voxel within the cube defined by xind, yind, and zind.
x = "dtiTensor": Returns a list with component names corresponding to what containing the specified statistics, i.e. fractional anisotropy "fa", geodesic anisotropy "ga", mean diffusivity "md", eigenvalues "evalues", main direction of anisotropy "andir", the tensor "tensor" the estimated S0 image "s0", the values of the model selection criteia BIC "bic" or AIC "aic" and/or the mask used to restrict computations "mask", as specified in argument what. Information is extracted for voxel within the cube defined by arguments xind, yind and zind.
x = "dwiMixtensor": Returns a list with component names corresponding to what containing the specified statistics. Possible values for what are "w0" (size of isotropic department), "order" (estimated number of mixture components), "eorder" effective order), "ev" (eigenvalues), "mix" (mixture weights), "andir" (main directions of diffusion), "fa" (FA index), "s0" (the estimated S0 image), the values of the model selection criteia BIC "bic" or AIC "aic" and mask (the mask used to restrict computations). Information is extracted for voxel within the cube defined by arguments xind, yind and zind.
x = "dwiQball": Returns an array containing the specified statistics, the estimated coefficients with respect to the selected spherical harmonics basis "sphcoef", the estimated S0 image "s0", the values of the model selection criteia BIC "bic" or AIC "aic" and/or the mask used to restrict computations "mask", as specified in argument what. Information is extracted for voxel within the cube defined by arguments xind, yind and zind.