Yes that's right.
Saad
On 30 Oct 2012, at 16:12, Michael Harms wrote:
> Hi Mark,
> You only get weighted least squares in dtifit if you use the -w or --wls
> options, right?
> That is, the default is ordinary least squares, right?
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> -----------------------------------------------------------
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: [log in to unmask]
>
>
>
>
> On 10/30/12 10:52 AM, "Mark Jenkinson" <[log in to unmask]> wrote:
>
>> Hi,
>>
>> To answer your other specific questions:
>>
>>> - Does it mean that FSL uses for eddy current correction a
>>> slice by slice correction (not a whole brain global affine
>>
>> FSL (i.e. eddy_correct) does _not_ do slice by slice correction. It
>> _does_ use a whole brain global affine correction. Essentially it just
>> runs FLIRT with 12 DOF, so referencing FLIRT is also worth doing.
>>
>>> - Manginšs paper describes the Geman-McLure M-estimator
>>> algorithm for the diffusion tensor estimation. Does FSL use this
>>> algorithm?
>>
>> Within the eddy current correction there is no diffusion tensor
>> estimation. It does weighted linear least squares inside dtifit.
>>
>> All the best,
>> Mark
>
--
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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