[Neuroimaging] [Nibabel] Public dataset generates unexpected

[Eleftherios Garyfallidis]

Clearly the title was meant to be "Public dataset generates unexpected
affine matrix" :)
Apologies,
Eleftherios

On Sun, Sep 10, 2017 at 1:31 PM Eleftherios Garyfallidis <elef at indiana.edu>
wrote:

> Hello Matthew and all,
>
> I downloaded a dataset from NITRC  by Boekel et al.
> https://www.nitrc.org/projects/dwi_test-retest/
>
> and I used nibabel to get the affine and voxel size. The authors claimed
> that the voxel size is 2x2x2mm^3 however the affine tells a different story.
>
> import nibabel as nib
>
> img = nib.load('pp26_dwi_run01_A.nii.gz')
>
> print(img.affine)
> [[  -1.999    0.047    0.077  108.292]
>  [   0.042    1.984   -0.471  -94.461]
>  [   0.047    0.251    3.703 -116.857]
>  [   0.       0.       0.       1.   ]]
>
> nib.affines.voxel_sizes(img.affine)
> *array([ 2.   ,  2.   ,  3.733])*
>
> The zoom function gives a different answer in agreement with the authors'
> claim.
>
> img.header.get_zooms()[:3]
> *(2.0, 2.0, 2.0)*
>
> Could it be that the authors damaged the header during preprocessing?
> I am assuming here that nibabel is bringing the correct information i.e.
> whatever is in the Nifti1 image.
>
> If you agree that this is an issue with the data itself. It would be nice
> to contact the authors.
>
> Best regards,
> Eleftherios
>
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