getTemplateCoordinates.Rd
This function will provide a mapping that labels an input image and its blobs.
getTemplateCoordinates( imagePairToBeLabeled, templatePairWithLabels, labelnames = NULL, outprefix = NA, convertToTal = FALSE )
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 |
The output point is in approximate template space.
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.
Avants, BB
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 ... # }