getTemplateCoordinates: Define an anatomical coordinate system in a new image based...

In neuroconductor-devel/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

Description

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

Usage

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

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.

Value

The output point is in approximate template space.

Author(s)

Avants, BB

Examples

## Not run: 
#
# 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 ...
#

## End(Not run)

neuroconductor-devel/ANTsR documentation built on April 1, 2021, 1:02 p.m.