getTemplateCoordinates¶

purpose:

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.

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

usage:

wcoords<-getTemplateCoordinates( list(bindtem,clust) , mymni , convertToTal = TRUE, outprefix = “/tmp/Q” )

examples:

#

# ch2bet is available in chris rorden's mricron

#  but you can do something with any other image

#  e.g. a statistical image

#

  tem<-antsImageRead('ch2bet.nii.gz',3)

  clust <- antsImageClone( tem )

  clust[ tem < 80 ]<- 0

  clust[ tem > 90 ]<- 0

  clust[  tem > 80 & tem < 90 ]<- 1

  ImageMath(3, clust,"ME",clust,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 ...

#

ANTsR 0.0.0 documentation

getTemplateCoordinates

getTemplateCoordinates¶