Useful code snippets Python

Set xyzt_units field of the NIfTI file to mm/s (BIDS format)

I want set xyzt_units field of the NIfTI file to mm/s:

from bids import BIDSLayout
import nibabel as nb

def set_xyzt_units(img, xyz='mm', t='sec'):
    header = img.header.copy()
    header.set_xyzt_units(xyz=xyz, t=t)
    return img.__class__(img.get_fdata().copy(), img.affine, header)    

def fix_xyzt_units(bids_root):
    layout = BIDSLayout(bids_root)
    for nii in layout.get(extension=['.nii', '.nii.gz']):
        metadata = layout.get_metadata(nii.path)
        img = nb.load(nii.path)
        fixed_img = set_xyzt_units(img)
        fixed_img.to_filename(nii.path)

fix_xyzt_units('path/to/your/bids/root')

Set repetition time in the NIfTI header using json file (BIDS format)

I want the repetition time in the NIfTI file header (pixdim[4]) to be equal to the value found in the associated json file:

  • All bold files will be explored

  • Old files are not overwritten, new images with an additional _fixed suffix will be created. After reviewing all the modified files, the user can manually overwrite the old files.

from pathlib import Path
from bids import BIDSLayout
import numpy as np

layout = BIDSLayout("path/to/your/bids/root")
bold_images = layout.get(suffix="bold", extension=[".nii", ".nii.gz"])
for bold in bold_images:
    TR = bold.get_metadata()["RepetitionTime"]
    img = bold.get_image()
    zooms = img.header.get_zooms()
    if not np.isclose(zooms[3], TR):
        old_path = Path(bold)
        new_path = old_path.with_name(f"{old_path.stem}_fixed.nii")
        img.header.set_zooms(zooms[:3] + (TR,))
        img.to_filename(new_path)