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

[Gabriel A. Devenyi]

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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