Many thanks!
nick
Niklas Lenfeldt, PhD, MSc, MAJ SWE A
Clinical Neuroscience, Umeå university
Phone: +46 70 609 66 87
Email: [log in to unmask]
-----Ursprungligt meddelande-----
Från: FSL - FMRIB's Software Library [mailto:[log in to unmask]] För Barbara Kreilkamp
Skickat: den 25 oktober 2015 20:08
Till: [log in to unmask]
Ämne: Re: [FSL] eddy v. eddy_correct
Hi Niklas,
Have had some limited experience with this comparison, but there is actually a publication on this, comparing eddy with topup and eddy_correct
http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0112411&representation=PDF
In my dataset I have seen that eddy_correct can introduce motion in participants that have not moved a lot. And just visually I am happier with eddy's (even without topup) performance than with eddy_correct as it seems to align the DWI much better.
If you can use eddy (if your bvectors were sampled on the whole sphere [check this with MATLAB commands mentioned here:
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY ], it would be good to do so.
Also, perhaps you have access to a T2w-image?
You might be able to follow this post on how to use the T2-w image in
topup:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A3=ind1303&L=FSL&E=quoted-printable&P=4254046&B=--B_3446959459_95180&T=text%2Fhtml;%20charset=UTF-8&pending=
Cheers,
Barbara
On 25/10/2015 18:32, Niklas Lenfeldt wrote:
> I have data that I previously applied eddy_correct to. Unfortunately, there are no repetitive b-0 volumes with reversed phase encoding, which, as I understand it, makes topup inapplicable.
>
> Is there any advantage to still apply eddy (although there is only one phase encoding) compared to eddy_correct (which already has been applied)?
>
> Best
>
> /Nick
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