Label multivariate components by an anatomical coordinate system. — getMultivariateTemplateCoordinates • ANTsR

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

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

Value

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

Details

Uses getTemplateCoordinates as a sub-routine.

TBN

Author

Avants, BB

Examples


if (FALSE) {
 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) )
}