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

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

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

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)

stnava/ANTsR documentation built on Sept. 19, 2024, 12:02 a.m.