Dear Tugan,
To measure the "magnitude of motion" I recommend the rmsdiff tool as it is
designed to do exactly that.
As for the rotate_bvecs script - this is not actually a script written by us (Oxford)
and so I cannot vouch for exactly how it works and how reliable it is. Hopefully it
has taken account of the exact nature of our particular decomposition, although
I personally favour using the matrix itself, rather than a decomposition if possible.
Someone else may be able to comment more on the use of avscale in rotate_bvecs.
All the best,
Mark
On 26 Oct 2011, at 22:29, Tugan Muftuler wrote:
> Hi,
>
> I was doing some exploration on gradient table correction for DTI and avscale output. Then I encountered an email from Mark Jenkinson (see below) that was warning users that the decomposition of the affine transformation matrix would not be unique. As I understand, the bvecs correction script is using avscale. I would be grateful if someone could comment on the reliability of such bvecs correction. I am also using avscale to generate a measure of "magnitude of motion". Would that be a reliable comparison across subjects?
>
> Best,
>
> Tugan
>
>
> -----Original Message-----
>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
>>> On Behalf Of Mark Jenkinson
>>> Sent: Monday, February 05, 2007 3:08 AM
>>> To: [log in to unmask]
>>> Subject: Re: [FSL] Flirt Transformation Matricies
>>>
>>> You can get *a* decomposition into angles using avscale.
>>> However, such decompositions are not unique (there are lots of
>>> arbitrary choices) so beware if you intend to compare these
>>> with anything else.
>>>
>>> All the best,
>>> Mark
>>>
>
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