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.

Author

Avants, BB

Examples

if (FALSE) { # \dontrun{
#
# 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 ...
#
} # }