getMultivariateTemplateCoordinates: Label multivariate components by an anatomical coordinate...

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

Label multivariate components by an anatomical coordinate system.

Description

This function will provide a mapping that labels the list of input images and each of their blobs.

Usage

getMultivariateTemplateCoordinates(
  imageSetToBeLabeledIn,
  templateWithLabels,
  labelnames = NULL,
  outprefix = NA,
  convertToTal = FALSE,
  pvals = NA,
  threshparam = 1,
  clustparam = 250,
  identifier
)

Arguments

imageSetToBeLabeledIn	a template paired with (most likely) the output of a multivariate sparse decomposition or (alternatively) could be just a statistical map with zeroes in non-interesting areas
templateWithLabels	e..g the mni image and brodmann label set
labelnames	a list of names for the labels
outprefix	if output to a file, provide file prefix
convertToTal	bool, return talairach coordinates
pvals	the already computed pvalue for each component
threshparam	for pvals
clustparam	for clusters
identifier	unique ID for this study

Details

Uses getTemplateCoordinates as a sub-routine.

TBN

Value

The output point coordinates are in approximate Talairach / MNI (or whatever) template space.

Author(s)

Avants, BB

Examples

## Not run: 
tem <- antsImageRead(getANTsRData("ch2"))
temlab <- antsImageRead(getANTsRData("ch2b"))
temlab2 <- antsImageRead(getANTsRData("ch2a"))
# try getANTsRData if you have www access
mymni <- list(
  antsImageRead(getANTsRData("mni"), 3),
  antsImageRead(getANTsRData("mnib"), 3),
  antsImageRead(getANTsRData("mnia"), 3)
)
mytem <- list(smoothImage(tem, 3), temlab, temlab2)
# mynetworkdescriptor<-getMultivariateTemplateCoordinates(
#  mytem, mymni , convertToTal = TRUE , pvals=c(0.01,0.05) )

## End(Not run)

stnava/ANTsR documentation built on April 16, 2024, 12:17 a.m.