[MINC-users] Computing a "orthogonalizing" rotation transform?

[Gabriel A. Devenyi]

Thanks Andrew, I was aware of this, this is messyness above and beyond
the sform/qform.

MRICron does this, for example.
--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com


On Wed, May 4, 2016 at 2:32 PM, Andrew Wood <andrew at biospective.com> wrote:
> Hi Gabriel,
>
> You might already be aware of this, but Nifti files can simultaneously
> encode two different world spaces (see qform and sform).  It's my
> understanding that the Nifti standard stately clearly how they're to be
> used, but many toolsets choose to not conform; one must be very careful
> when using tools coming from different nifti toolkits.
>
> Here's an example where the qform/sform issue could lead to confusion: a
> viewer could use the sform to position the image in the viewer, but then a
> nifti-minc converter could pick up the qform to generate the world axes;
> the sform orientation information would then be lost.
>
> Not sure if that helps, but it could be related.
>
> Cheers,
> Andrew
>
> On Wed, May 4, 2016 at 2:13 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
> wrote:
>
>> Thanks Andrew/Vlad,
>>
>> Vlad: that's a good question, I think what the apps are doing is
>> computing the principal axes of the volume distribution, and aligning
>> those with the slice directions
>>
>> Andrew: thanks, that's helpful if I ever run into that case.
>> --
>> Gabriel A. Devenyi B.Eng. Ph.D.
>> Research Computing Associate
>> Computational Brain Anatomy Laboratory
>> Cerebral Imaging Center
>> Douglas Mental Health University Institute
>> Affiliate, Department of Psychiatry
>> McGill University
>> t: 514.761.6131x4781
>> e: gdevenyi at gmail.com
>>
>>
>> On Wed, May 4, 2016 at 1:44 PM, Andrew Wood <andrew at biospective.com>
>> wrote:
>> > Hi Gabriel,
>> >
>> > I think you need to resample the image such that the voxel lattice lines
>> up
>> > with the world dimensions. Would this do it?
>> >
>> > $ mincresample in.mnc -dircos 1 0 0  0 1 0  0 0 1 out.mnc
>> >
>> > - Andrew
>> >
>> >
>> > On Wed, May 4, 2016 at 1:36 PM, Vladimir S. FONOV <
>> vladimir.fonov at gmail.com>
>> > wrote:
>> >
>> >> What is the definition of orthogonalized view?
>> >>
>> >> perhaps itk_resample --uniformize 1 will do it for you?
>> >>
>> >>
>> >>
>> >> On 16-05-04 01:22 PM, Gabriel A. Devenyi wrote:
>> >>
>> >>> Hi minc-users,
>> >>>
>> >>> Many nifti tools are "helpful" in that they orthogonalize your view
>> >>> relative to the principal axes they compute from a native scan on
>> >>> load. This makes it hard to compare to Display.
>> >>>
>> >>> Obviously, Display doesn't do this, but is there a tool or method to
>> >>> compute such a transform so I can apply it to a MINC file?
>> >>>
>> >>> Thanks!
>> >>>
>> >>> --
>> >>> Gabriel A. Devenyi B.Eng. Ph.D.
>> >>> Research Computing Associate
>> >>> Computational Brain Anatomy Laboratory
>> >>> Cerebral Imaging Center
>> >>> Douglas Mental Health University Institute
>> >>> Affiliate, Department of Psychiatry
>> >>> McGill University
>> >>> t: 514.761.6131x4781
>> >>> e: gdevenyi at gmail.com
>> >>> _______________________________________________
>> >>> MINC-users at bic.mni.mcgill.ca
>> >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >>>
>> >>>
>> >>
>> >> --
>> >> Best regards,
>> >>
>> >>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>> >> _______________________________________________
>> >> MINC-users at bic.mni.mcgill.ca
>> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >>
>> > _______________________________________________
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