pythonpathmrinibabel

Nibabel cannot read gz file


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":

1


Solution

  • 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