The function takes two objects, fiberobj with class 'dwiFiber' containing
fiber tracking results and an array or nifti-object containing atlas information.
For each combination of regions defined in the atlas the number of fibers connecting these
regions is calculated, resulting in a matrix of fiber counts. As default this matrix
is standardized and the diagonal elements are set to zero.
AdjacencyMatrix(fiberobj, atlas, labels = NULL,
method = c("standardize", "counts"), diagelements = FALSE,
symmetric=TRUE, verbose = FALSE)A matrix with dimensions equal to the number of regions defined in the atlas
and dimnames given by labels or by the region number. The matrix contains
fiber counts or values standardized with the number of fibers ni, nj
originating/ending from the pair of regions. Depending on symmetric standardization
is with 1/sqrt(ni*nj) or with 1/ni.
an object of class 'dwiFiber'
an object of class 'array' or 'nifti' containing region indices as
intensities. The atlas needs to be registered to DWI (subject) space,
with array dimension corresponding to fiberobj@ddim
optional labels for the regions. Will be used as dimnames of the resulting matrix.
either "standardize" or "counts", determines if fiber counts
or a standardized (default) matix is returned.
logical, if FALSE the diagonal elements of the standardized matrix are set to zero (default).
logical, with ni the number of fibers originating if FALSE standardized values
counts(i,j)/ni,
if TRUE we get counts(i,j)/sqrt(nj*nj).
logical, if TRUE report pairwise fiber counts.
Joerg Polzehl polzehl@wias-berlin.de
dwiFiber