skiftiTools (version 0.1.0)

Skifti2Nifti: Create a Nifti file from Skifti data

Description

Skeleton mask and corresponding image intensity data in Nifti format. The skeleton mask is used to determine the coordinates of intensity data. If optional label file is given, that is used to label the voxels.

Usage

Skifti2Nifti(Skifti_data)

Value

Nifti skeleton file for Skifti data

Arguments

Skifti_data

Intensity data in Nifti format

Examples

#source('../../R/Skifti2Nifti.R')
#source('../../R/Nifti2Skifti.R')
library(RNifti)
data<-array(0,dim=list(10,10,10,10))
for(t in 1:10) {
  for(x in 1:10) {
    for(y in 1:10) {
      for(z in 1:10) {
        data[x,y,z,t]<-t+x
      }
    }
  }
}
data_Nifti<-RNifti::retrieveNifti(data)
RNifti::writeNifti(data_Nifti, "data_Nifti.nii.gz", template = NULL, datatype = "auto")

data_skeleton<-array(0,dim=list(10,10,10))
data_skeleton[5,5,5]<-1
data_skeleton[6,6,6]<-1
data_skeleton[7,7,7]<-1
data_skeleton_Nifti<-RNifti::retrieveNifti(data_skeleton)
RNifti::writeNifti(data_skeleton_Nifti, "data_skeleton_Nifti.nii.gz", datatype = "auto")

data_Skifti<-Nifti2Skifti(Nifti_data="data_Nifti.nii.gz", 
                          Nifti_skeleton="data_skeleton_Nifti.nii.gz", 
                          selected_volumes=c(1), 
                          Nifti_labels=NULL, 
                          write_coordinates=TRUE, 
                          verbose=FALSE)

# Create Skifti
data_Nifti2<-Skifti2Nifti(data_Skifti)
RNifti::writeNifti(data_Nifti2[[1]], "data_Nifti.nii.gz", datatype = "auto")
data_Nifti2<-RNifti::readNifti("data_Nifti.nii.gz", internal = TRUE, volumes = NULL)