Convert .h5 to .nii.gz

h5_to_niigz.py

# this snippet shows how to convert a .h5 transformation to a .nii.gz displacement field using the ants python library
# based on this commend https://github.com/ANTsX/ANTs/issues/54#issuecomment-2085595485
# to do this, we need the reference/fixed image and the .h5 transformation

from ants import utils as utils_ants


args = ['-d', '3',
        '-r', 'reference.nii.gz',
        '-t', 'transform.h5',
        '-o', '[ transform.nii.gz, 1 ]',
        '--verbose']

libfn = utils_ants.get_lib_fn('antsApplyTransforms')

libfn(processed_args)