Nrrd to Nifti file conversion

Question

I am looking to convert ~1000 .nrrd files into Nifit (.nii.gz) format. I've been using 3DSlicer's ResampleScalarVectorDWIVolume command-line module to accomplish this task. But this process is really slow. It takes ~4 minutes to convert each file on my system. I was wondering what tool do people use for such conversions?

Answer 1

The following code can be used for converting all the '.nrrd' files in a folder into compressed 'nifti' format:

import os
from glob import glob
import nrrd #pip install pynrrd, if pynrrd is not already installed
import nibabel as nib #pip install nibabel, if nibabel is not already installed
import numpy as np

baseDir = os.path.normpath('path/to/file')
files = glob(baseDir+'/*.nrrd')

for file in files:
#load nrrd 
  _nrrd = nrrd.read(file)
  data = _nrrd[0]
  header = _nrrd[1]

#save nifti
  img = nib.Nifti1Image(data, np.eye(4))
  nib.save(img,os.path.join(baseDir, file[-8:-5] + '.nii.gz'))

For example, this script would convert abc.nrrd and xyz.nrrd files in the baseDir to abc.nii.gz and xyz.nii.gz respectively.