Hi
I think rotate_bvecs uses the whole matrix, not the angles.
Saad.
On 27 Oct 2011, at 09:11, Mark Jenkinson wrote:
> Dear Tugan,
>
> The problem is that there are many different *definitions* of rotation angles.
> It isn't that our tool might give different answers when run different times, it
> is that it uses a convention which might not be the same as other software
> or the conventions that you are expecting. For instance, we decompose the
> rotation matrix as: R = Rx * Ry * Rz (where Rx is rotation about the x-axis, etc.)
> This could easily be R = Rz * Ry * Rx instead, and because 3D rotations do not
> commute you get *different* answers for the rotation angles when using different
> conventions like this.
>
> So it wouldn't matter if you got the angles from avscale of flirt or any other
> method at all. The problem is that there is no single, unique *definition* of
> what the angles should be for a given rotation matrix (similar things exist for
> skews/scales) and so you can only ever get a decomposition for some
> arbitrarily chosen convention/definition.
>
> As long as you use the angles consistently with whatever processing you are
> doing later then it is OK. The thing is to be careful that you understand the
> conventions fully before using the angles. For this reason I prefer to stick
> with the matrices whenever possible, and avoid such arbitrary decompositions.
>
> All the best,
> Mark
>
>
>
>
>
> On 27 Oct 2011, at 04:46, Tugan Muftuler wrote:
>
>> Dear Mark,
>>
>> Many thanks for the clarification and the rmsdiff tool. Certainly a useful tool that escaped my attention.
>>
>> In addition to quantifying the amount of motion, I also want to obtain the rotation angles of the affine transformation separately. I browsed through FSL email archives and FLIRT pages but I cannot find a better answer to this other than avscale. Since you mentioned that decomposition by avscale may not produce unique results, is it possible to command FLIRT to report rotation angles when i run it on my data? This way I can ensure that the bvecs are accurately oriented.
>>
>> best regards,
>>
>> Tugan
>>
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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