Define an anatomical coordinate system in a new image based on a template

This function will provide a mapping that labels an input image and its blobs.

getTemplateCoordinates(
  imagePairToBeLabeled,
  templatePairWithLabels,
  labelnames = NULL,
  outprefix = NA,
  convertToTal = FALSE
)

Arguments

imagePairToBeLabeled	e.g. the template image and the activation map
templatePairWithLabels	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

Value

The output point is in approximate template space.

Details

Uses Matthew Brett's mni2tal to get the final Talairach coordinates from MNI space.

This is a standard approach but it's not very accurate.

Examples

if (FALSE) {
#
# ch2bet is available in chris rorden's mricron
#  but you can do something with any other image
#  e.g. a statistical image
#
  tem<-antsImageRead(getANTsRData("ch2"),3)
  clust <- antsImageClone( tem )
  atem = as.array(tem)
  clust[ atem < 80 ]<- 0
  clust[ atem > 90 ]<- 0
  clust[  atem > 80 & atem < 90 ]<- 1
  clust<-iMath(clust,"ME",1)  # erosion
  clust <- labelClusters( clust , minClusterSize=30, minThresh=1, maxThresh=1)
  if ( ! exists("mymni") ) {
  # try getANTsRData if you have www access
    mymni<-list( antsImageRead(getANTsRData("mni"),3),
                 antsImageRead(getANTsRData("mnib"),3),
                 antsImageRead(getANTsRData("mnia"),3) )
  }
  template_cluster_pair<-list(tem,clust)
  gcoords<-getTemplateCoordinates( template_cluster_pair ,
      mymni , convertToTal = TRUE )
# output will be like
# > gcoords$templatepoints
#     x   y   z t label Brodmann                 AAL
# 1  -12  13  -3 0     1        0           Caudate_R
# 2   13  16   5 0     2        0           Caudate_L
#
# can also use a white matter label set ...
#
}