T1w to MNI transformation with ANTS apply transforms

apply_ants_transform.py

from nipype.interfaces.ants import ApplyTransforms

# necessary files
norm_template = root + '/derivatives/mni152_bet.nii'  
ants_transforms = sorted(glob(root + 'derivatives/fmriprep/sub-*/anat/sub-*_T1w_target-MNI152NLin2009cAsym_warp.h5'))

# files to transform from T1w to MNI
copes = sorted(glob(root + 'derivatives/analysis/sub-*/video/betaseries/level_2.gfeat/cope1.feat/stats/cope1.nii.gz'))

# loop and transform files for all participants
for s in range(nr_sub):
    fname = copes[s]
    con_norm = fname.replace('.nii.gz', '_inMNI.nii.gz')

    ApplyTransforms(
        reference_image=norm_template,
        input_image_type=3,
        float=True,
        interpolation='NearestNeighbor',
        invert_transform_flags=[False],
        output_image=con_norm,
        input_image=fname,
        transforms=[ants_transforms[s]]).run()