[Neuroimaging] [Nibabel] Public dataset generates unexpected
elef at indiana.edu
Tue Sep 12 10:58:20 EDT 2017
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>
> Thanks for the feedback Matthew.
> Here is also a script that corrects another problem in the DWI data. There
> the last bvector is incorrect.
> 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).
> On Sun, Sep 10, 2017 at 4:04 PM Eleftherios Garyfallidis <elef at indiana.edu>
>> Clearly the title was meant to be "Public dataset generates unexpected
>> affine matrix" :)
>> 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.
>>> 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')
>>> [[ -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. ]]
>>> *array([ 2. , 2. , 3.733])*
>>> The zoom function gives a different answer in agreement with the
>>> authors' claim.
>>> *(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,
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