extract the first volume of nifti file for every participant

nibabel_extract_one_volume.py

from glob import glob
import nibabel as nib
import numpy as np

root='path'
subject_ids = [s[-6:] for s in sorted(glob(root + 'sub-*'))] # to get subject ids in format sub-01

# load the functional files for every participant
funcs = sorted(glob(root+'fmriprep/sub-*/func/sub-*_task-x_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz'))

for c, func in enumerate(funcs):
    out_name = root + subject_ids[c] + '/example_func.nii.gz'
    img = nib.load(func)
    img_data = img.get_data()
    example_img = img_data[:, :, :, 0]
    out_data = nib.Nifti1Image(example_img, header=img.header, affine=img.affine)
    nib.save(out_data, out_name)
    print('data for ', subject_ids[c], ' is saved')