[Neuroimaging] why 2 affine transforms in the nifti

Demian Wassermann demian.wassermann at inria.fr
Fri Jul 9 05:13:31 EDT 2021

Dear Romain,

I think that you refer to the qform and sform transforms. If I’m not wrong the main idea of storing these two transforms is that qform transforms between voxel space and subject space in mm, and that sform transforms between voxel space and a “standard space” such as ACPC, or talairach (see https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html ) so you’d encode the output of a linear registration towards such standard space. Then there is of course the issue of poor documentation and then the way the data is used despite the standard’s intent

Demian Wassermann, PhD, HdR
demian.wassermann at inria.fr
Associate Research Professor (CRCN)
Parietal Team
INRIA Saclay Ile-de-France
1 Rue Honoré d'Estienne d'Orves, 91120 Palaiseau

> On 9 Jul 2021, at 10:51, VRomain <romain.valabregue at upmc.fr> wrote:
> Hello
> As suggest by oscar I open a new thread, since there may be nothing to do with Nibabel CZI grant
> So to resume, I sometimes get  troubles when playing with different software, because of the 2 affines stored in the nifti file.
> (some software thing one should only read / write the sform, other the qform, so it is easy to get to inconsistency, that will just scratch your results)
> Thanks @ oscar to point out the nitransforms repo - https://github.com/poldracklab/nitransforms <https://github.com/poldracklab/nitransforms>)
> I'll have a closer look, this is indeed an important objectiv
> I am curious, to know why it was a clever idea to store 2 affine ? ( I probably miss the point ... )
> From what I understand, it was meant to get an history of the registration made on the data. The only software I know that use it, is spm coregister function. they update the sform and keep the qform. Ok we can come back, but if for any reason one have to coregister a second time, then the information is lost (because they chose to update the sform, and the qform take the old sform value ...)
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