Image orientation error in ITKsnap

A workaround is to reset the header information:

headertool input_image_nifti output_image_nifti -reset
headertool input_segmentation_nifti output_segmentation_nifti -reset

In R:

irtk_exe_dir<-("C:/irtk")
headertool<-paste(irtk_exe_dir,"/headertool ",sep="")

setwd(cur_dir)
filenames<-grep(list.files(cur_dir), pattern='[txt,m]', inv=T, value=T)
filenames

for (j in filenames){file_dir<-file.path(cur_dir,j)
                     setwd(file_dir)
                     shell(paste(headertool,"LVSA.nii.gz"," LVSA.nii.gz -reset")}