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- import nibabel as nb
- from pathlib import Path
- def sanitize(input_fname):
- im = nb.as_closest_canonical(nb.load(str(input_fname)))
- hdr = im.header.copy()
- dtype = 'int16'
- if str(input_fname).endswith('_mask.nii.gz') or str(input_fname).endswith('_dseg.nii.gz'):
- dtype = 'uint8'
- hdr.set_data_dtype(dtype)
- nii = nb.Nifti1Image(im.get_data().astype(dtype), im.affine, hdr)
- sform = nii.header.get_sform()
- nii.header.set_sform(sform, 4)
- nii.header.set_qform(sform, 4)
- nii.header.set_slope_inter(slope=1.0, inter=0.0)
- nii.header.set_xyzt_units(xyz='mm')
- # print(nii.shape)
- # print(nii.affine)
- nii.to_filename(str(input_fname))
- for f in Path().glob('tpl-*.nii.gz'):
- print('Sanitizing file %s' % f)
- sanitize(f)
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