I am working with images in the format nii.gz. Therefore, I am using nibabel in order to open them. The problem is that when I open the images, transform them to numpy arrays and convert them back to Nifti format, the output size is changed. The sequence is:
nifti_image = nib.load('/my_path_to_image/image.nii.gz')
np_img = ct_images.get_fdata()
nifti_final = nib.Nifti1Image(data, affine=np.eye(4)) # Convert them to nifti
nib.save(nifti_final , 'image.nii.gz')
The initial file is ~45 MB, after running the code above, the image is ~65 MB. I know that the original images are 16-bit encoded. My initial theory was that when transforming to numpy array, they were encoded as 64-bit which is indeed the case. So I tried the following:
nifti_image = nib.load('/my_path_to_image/image.nii.gz')
np_img = ct_images.get_fdata()
np_img = np_img.astype(numpy.float16, copy=False)
nifti_final = nib.Nifti1Image(data, affine=np.eye(4)) # Convert them to nifti
nib.save(nifti_final , 'image.nii.gz')
However, the ouput is still the same size ~65MB. Any ideas why this is happening?
You should add the original nifti affine and header information to the output nifti. E.g., in your case:
nifti_final = nib.Nifti1Image(data, nifti_image.affine, nifti_image.header)