Convert NIfTI images into multiple TIF images

nii_to_tif.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
nii_to_tif

command line executable to convert 3d nifti images to 
individual tiff images along a user-specified axis

call as: python nii_to_tif.py /path/to/nifti /path/to/tif
(append optional arguments to the call as desired)

Author: Jacob Reinhold (jacob.reinhold@jhu.edu)
"""

import argparse
from glob import glob
import os
import sys

from PIL import Image
import nibabel as nib
import numpy as np


def arg_parser():
    parser = argparse.ArgumentParser(description='split 3d image into multiple 2d images')
    parser.add_argument('img_dir', type=str, 
                        help='path to nifti image directory')
    parser.add_argument('out_dir', type=str, 
                        help='path to output the corresponding tif image slices')
    parser.add_argument('-a', '--axis', type=int, default=2, 
                        help='axis of the 3d image array on which to sample the slices')
    parser.add_argument('-p', '--pct-range', nargs=2, type=float, default=(0.2,0.8),
                        help=('range of indices, as a percentage, from which to sample ' 
                              'in each 3d image volume. used to avoid creating blank tif '
                              'images if there is substantial empty space along the ends '
                              'of the chosen axis'))
    return parser


def split_filename(filepath):
    path = os.path.dirname(filepath)
    filename = os.path.basename(filepath)
    base, ext = os.path.splitext(filename)
    if ext == '.gz':
        base, ext2 = os.path.splitext(base)
        ext = ext2 + ext
    return path, base, ext


def main():
    try:
        args = arg_parser().parse_args()
        fns = glob(os.path.join(args.img_dir, '*.nii*'))
        for fn in fns:
            _, base, ext = split_filename(fn)
            img = nib.load(fn).get_data().astype(np.float32).squeeze()
            if img.ndim != 3:
                print(f'Only 3D data supported. File {base}{ext} has dimension {img.ndim}. Skipping.')
                continue
            start = int(args.pct_range[0] * img.shape[args.axis])
            end = int(args.pct_range[1] * img.shape[args.axis])
            for i in range(start, end):
                I = Image.fromarray(img[i,:,:], mode='F') if args.axis == 0 else \
                    Image.fromarray(img[:,i,:], mode='F') if args.axis == 1 else \
                    Image.fromarray(img[:,:,i], mode='F')
                I.save(os.path.join(args.out_dir, f'{base}_{i:04}.tif'))
        return 0
    except Exception as e:
        print(e)
        return 1


if __name__ == "__main__":
    sys.exit(main())

@sujeongEOM see up above (e.g., here) for a discussion of this issue.