Thanks for a quick reply Jesper.
Imagined you would checked it for high-bvalues. Are there any lower
SNR-levels to be above though?
Is there anything one should think of when generating a gradient
scheme to make a good sampling? The half-sphere scheme on your website
(http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY) looks very uniform.
I will pilot the twice-refocusing to see, but it would be tempting to
shorten the TE as we have strong gradients and would be able to get in
the weighting without needed to separate diffusion gradients too much.
Cheers,
Finn
On 30 August 2013 15:04, Jesper Andersson
<[log in to unmask]> wrote:
> Dear Finn,
>
>>
>> I am wondering about the topup-eddy tools in FSL. Have used
>> eddy_correct before with older "b=1000-data". Now I am going to
>> collect some high-bvalue data, well one-shell with b=3000. My patient
>> population could be prone to some motion, so I need motion correction.
>> The DWI data is going to be used for fibre tracking of the optic
>> radiation with some HARDI-technique, so I will aim for b-value around
>> 3000. Can fit in 60 gradient directions, and would not want to collect
>> any unnecessary b0:s.
>>
>> I have not set the protocol. I have the possibility to change the
>> PE-blip directions and to tailor a gradient scheme.
>>
>> Some questions:
>>
>> How does topup-eddy work for higher b-values. Enough signal/contrast
>> in the images with b=3000 data for distortion-, eddy- and motion
>> correction? Any experience of topup-eddy at these b-values?
>
> We routinely use it on b-values of ~3000 and when we have tested it on b-values up to 10000 it has worked well.
>
>> How many b0:are needed for topup? Do eddy also use the b0:s?
>
> Acquire at least two for each PE-direction. Topup only really needs one of each, so it is more a matter of not putting all your eggs in one basket in case for example the subject makes a sudden movement dusting the acquisition of the b0.
>
>> Is it still advisable to use a twice-refocused SE to limit eddy
>> currents? Or can I omit this and go for shorter TE and hope that eddy
>> sorts it?
>
> We have gone with the latter for the HCP project. If I were you I should pilot it first though to make sure it works as well on your data.
>
> Jesper
>
>
>>
>> Cheers,
>> Finn Lennartsson
--
_______________________________
Finn Lennartsson
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SE-34393 Älmhult, Sweden
Cell: + 46 704 838907
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