skiftiTools (version 0.1.0)

Nifti2Skifti: Create a SKIFTI file from fsl TBSS skeleton data

Description

Skeleton mask and corresponding image intensity data must be 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

Nifti2Skifti(
  Nifti_data = NULL,
  Nifti_skeleton = NULL,
  selected_volumes = NULL,
  Nifti_labels = NULL,
  write_coordinates = FALSE,
  verbose = FALSE
)

Value

skifti object with default rownames as vol1, vol2 .... volN as indexes from the nifti data

Arguments

Nifti_data

Intensity data in Nifti format (required)

Nifti_skeleton

Skeleton at same imaging space as the data, in Nifti format (required)

selected_volumes

Selected volume indexes starting from 1 (default==NULL, selecting all)

Nifti_labels

Labeling data to be used inside mask, writing extra line to the output about labels (default==NULL, no extra labeling)

write_coordinates

TRUE/FALSE(default) write coordinates of voxels in x,y,z ASCII format, in the same order as they appear in the skifti

verbose

TRUE/FALSE(default) for verbose messages

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)