[Neuroimaging] [Nibabel] Public dataset generates unexpected

[Eleftherios Garyfallidis]

Done! Contacted the authors and they are now working to fix the issues.

Will post here when the corrected data go online.

On Sun, Sep 10, 2017, 5:08 PM Eleftherios Garyfallidis <elef at indiana.edu>
wrote:

>
> Thanks for the feedback Matthew.
>
> Here is also a script that corrects another problem in the DWI data. There
> the last bvector is incorrect.
>
> https://gist.github.com/Garyfallidis/199813624bb6d2dac3f51aa6b41717af
>
> I will send the authors an e-mail with both issues.
> For the first issue I think they used some tool that does not contain the
> affine after reslicing.
> Probably the original data have an actual resolution of 2x2x3.7 which is
> not ideal for tracking (even after reslicing).
>
> Cheers,
> Eleftherios
>
> On Sun, Sep 10, 2017 at 4:04 PM Eleftherios Garyfallidis <elef at indiana.edu>
> wrote:
>
>> 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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