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

[bthirion]

I would indeed try nilearn.image.resample_img()
B
On 18/08/2017 23:28, Christopher Markiewicz wrote:
> Hi Michael,
>
> At first glance this looks reasonable to me, so if I were to try to 
> figure out the issue, I'd probably end up digging through nilearn's 
> image resampling, which uses ndimage.affine_transform under the hood 
> [0]. It's a much more flexible function that what you're looking for, 
> but I think you should be able to find what you need in all of that.
>
> I'm also pretty sure that, with a nipy image, you can do this with 
> `img[::2, ::2, ::2]`, but not sure quite where to point you to in that 
> codebase.
>
> Chris
>
> [0] 
> https://github.com/nilearn/nilearn/blob/master/nilearn/image/resampling.py#L221-L271
>
> On Fri, Aug 18, 2017 at 4:52 PM, Michael Waskom <mwaskom at nyu.edu 
> <mailto: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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