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NIfTI: default back to sform in case of mismatch #1540

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jdtournier commented Jan 29, 2019

See discussion at http://community.mrtrix.org/t/inconsistent-qform-sform-on-nifti-image/1663/9
Carries on from #1212

We should also discuss further about the possibility of zeroing the qform on write if it doesn't match the sform (should only happen for non-rigid transforms).

Also should add FAQ section in the docs about this.

@jdtournier jdtournier self-assigned this Jan 29, 2019
@jdtournier jdtournier added this to the MRtrix3 3.0 release milestone Jan 29, 2019
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Lestropie commented Jan 29, 2019

We should also discuss further about the possibility of zeroing the qform on write if it doesn't match the sform (should only happen for non-rigid transforms).

Not sure it needs discussion; I think it's pretty clear that this is the best behaviour.

jdtournier added 11 commits Apr 16, 2019
- removed Analyze format handler, since already handled by NIfTI-1.1
- consolidated all operations into generic template class to share as
  much code as possible between NIfTI-1.1 and 2 handling.
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jdtournier commented Apr 17, 2019

OK, I reckon this one is good to go, if someone finds the time to have a look at it. Might need to double-check that I haven't borked anything up with all the changes to the NIfTI handling... Are there any known NIfTI validation sets that can be used for this...?

@jdtournier jdtournier requested a review from MRtrix3/mrtrix3-devs Apr 17, 2019
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Lestropie commented Apr 17, 2019

Are there any known NIfTI validation sets that can be used for this...?

Not that I'm already aware of. We could derive something but we'd probably need some sort of cross-checking with fslhd and mri_info.

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jdtournier commented May 8, 2019

OK, this isn't as straightforward as I'd like... The handling of what happens to the voxel sizes when you have a non-orthonormal transform is inconsistent between NIfTI and mif. This is going require a bit more thought...

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