DTI_resample.py

import nibabel as nb
import numpy as np
from nilearn.image import resample_img
import pp
from glob import glob
import os
import re

def main():
    workshopDataLoc = '/media/workshop/openData_for_workshop/NITRC/workshop'
    subjects = [x for x in os.listdir(workshopDataLoc) if x.startswith('subj')]

    for subject in subjects:
        print subject
        subj_DTI_in = glob(os.path.join(workshopDataLoc, subject, 'DTI/*DTI.nii'))[0]
        subj_DTI_out = re.sub('DTI.nii', 'DTI-resampled.nii.gz', subj_DTI_in)

        resample(subj_DTI_in, subj_DTI_out)
        #print subj_DTI_in, subj_DTI_out

def resample(inputImg, outputImg, vsize=[2.3,2.3,2.3]):
    image_to_resample = nb.load(inputImg)
    desired_affine = np.diag(vsize)
    resampled_image = resample_img(image_to_resample,
                                   target_affine=desired_affine)
    resampled_image.to_filename(outputImg)

if __name__=='__main__':
    main()