Example of reading and writing a NIfTI file with nibabel

nifti_readwrite.py

"""
Program nifti_readwrite.py
Sep 16, 2019
David Gobbi
"""

import sys
import argparse
import nibabel as nib

def main(argv):
    """Callable entry point.
    """
    parser = argparse.ArgumentParser(prog=argv[0])
    parser.add_argument('-i', '--input', required=True, help="Input file.")
    parser.add_argument('-o', '--output', required=True, help="Output file.")
    args = parser.parse_args(argv[1:])

    # read the input image
    infile = nib.load(args.input)
    # get the data, undo the transpose
    data = infile.get_data().T
    # get x, y, z spacing (in that order)
    pixdim = infile.header['pixdim'][1:4]

    # index into the image with "data[z,y,x]" (z index comes first)

    # create an output file with the same transform and header as input
    outfile = nib.Nifti1Image(data.T, infile.affine, header=infile.header)
    nib.save(outfile, args.output)

if __name__ == '__main__':
    r = main(sys.argv)
    if r is not None:
        sys.exit(r)