Nibabel cannot read gz file

Question

im trying to load my image with nibabel, but I keep getting an "ImageFileError". kindly note that my image is in .gz format. I get the error "file is not a gzip file":

Answer 1

I had the same issue for a subject from the ADNI (Alzheimer's Disease Neuroimaging Initiative) dataset.

What worked for me was to load it with SimpleITK and saving it again (overwriting) still with SimpleITK. Here's the code:

import SimpleITK as sitk

path_corrupted_nifti = "path/to/img.nii.gz"
sitk_img = sitk.ReadImage(path_corrupted_nifti)  # load with sitk
sitk.WriteImage(sitk_img, path_corrupted_nifti)  # overwrite

after doing this, I was able to load the volume also with nibabel