[Neuroimaging] [Nibabel] up/downsample image in Python

[Satrajit Ghosh]

hi michael,

for downsampling, you should really consider an anti-aliasing filter. i
don't believe zoom uses one.

https://en.wikipedia.org/wiki/Image_scaling

cheers,

satra

On Sat, Aug 19, 2017 at 4:52 AM, Michael Waskom <mwaskom at nyu.edu> wrote:

> Hi Matthew/Chris/others,
>
> Building on my previous question, I would also like to implement a
> pure-python downsampling of my images. I have done:
>
> import nibabel as nib
> from scipy import ndimage
> img = nib.load("brain.nii")
> data = img.get_data()
> lowres_data = ndimage.zoom(data, .5)
> zoom_xfm = np.eye(4)
> zoom_xfm[:3, :3] /= .5
> lowres_affine = img.affine.dot(zoom_xfm)
> lowres_img = nib.Nifti1Image(lowres_data, lowres_affine, img.header)
> lowres_img.to_fileame("lowres_brain.nii")
>
> This is very close, but when I view the resulting image in Freeview (my
> downsampled image is also slightly stretched relative to the anatomical).
>
> I can also compare to the result from mri_convert, i.e. mri_convert
> brain.nii -vs 2 2 2 lowres_brain.nii. The resulting image is not
> stretched relative to the hires brain, so it's not an artifact on
> Freeview's side. The images also don't have an identical affine (it is off
> by 0.5 in the third row of the final column.
>
> What am I missing about how to alter to affine of a downsampled image?
> Alternative, is ndimage.zoom not the right Python function to use here?
>
> Best,
> Michael
>
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