skiftiTools (version 0.1.0)

Skifti2CSV: 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

Skifti2CSV(Skifti_data, filename, overwrite = FALSE, sep = ";")

Value

CSV filename

Arguments

Skifti_data

Intensity data in Nifti format

filename

file to read'

overwrite

TRUE/FALSE(default) to overwrite existing data

sep

file separator to be written default ';'

Examples

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=1:10, 
                          Nifti_labels=NULL, 
                          write_coordinates=TRUE, 
                          verbose=FALSE)

Skifti2CSV(data_Skifti, "data_Skifti.csv", overwrite=TRUE, sep=';')
data_csv<-read.csv2("data_Skifti.csv", ';', header = FALSE, row.names = NULL)