CODEWITHSUNDEEP
pythonnifti
avi.ks
avi.ks

Reputation: 77

Nrrd to Nifti file conversion

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?

Upvotes: 1

Views: 8817

Answers (3)

kdebugging
kdebugging

Reputation: 561

Similar to avi.ks's answer, but in case anyone needs to preserve the header information:

import glob
import nibabel as nib
import nrrd

# Get a list of .nrrd files in a directory
nrrd_files = glob.glob('path/to/nrrd/directory/*.nrrd')

# Loop through each .nrrd file
for nrrd_file in nrrd_files:
    # Read the .nrrd file
    data, header = nrrd.read(nrrd_file)
    
    # Create a NIfTI1Image object
    nifti_img = nib.Nifti1Image(data, affine=None)
    
    # Update the NIfTI header with necessary information
    nifti_img.header.set_data_dtype(data.dtype)
    nifti_img.header.set_zooms(header['space directions'])
    
    # Generate the output .nii file path by replacing the extension
    nii_file = nrrd_file.replace('.nrrd', '.nii')
    
    # Save the NIfTI1Image object as .nii file
    nib.save(nifti_img, nii_file)

In this code, I use header['space directions'] from the .nrrd header to set the pixel spacing in the NIfTI header using nifti_img.header.set_zooms(). You might need to adjust the header['spcace direction'] dimension. In my case I change it to :

nifti_img.header.set_zooms([header['space directions'][0, 0],
                            header['space directions'][1, 1],
                            header['space directions'][2, 2]])

Upvotes: 0

lei
lei

Reputation: 71

import vtk

def readnrrd(filename):
    """Read image in nrrd format."""
    reader = vtk.vtkNrrdReader()
    reader.SetFileName(filename)
    reader.Update()
    info = reader.GetInformation()
    return reader.GetOutput(), info

def writenifti(image,filename, info):
    """Write nifti file."""
    writer = vtk.vtkNIFTIImageWriter()
    writer.SetInputData(image)
    writer.SetFileName(filename)
    writer.SetInformation(info)
    writer.Write()

m, info = readnrrd('/media/neubias/b0c7dd3a-8b12-435e-8303-2c331d05b365/DATA/Henry_data/mri.nrrd')
writenifti(m, '/media/neubias/b0c7dd3a-8b12-435e-8303-2c331d05b365/DATA/Henry_data/mri_prueba2.nii', info)

Upvotes: 7

avi.ks
avi.ks

Reputation: 77

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.

Upvotes: 4

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