You could also always skullstrip the b0 if you think that is the cause of
the issue.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Steve Smith
Sent: Thursday, May 01, 2008 12:03 AM
To: [log in to unmask]
Subject: Re: [FSL] Misregistration after eddy_correct
Hi,
We've not seen this behaviour but it's possible, particularly if you
have low image intensities (e.g. because your b-value is high). You
could play with different target images, yes, and you could also try
reducing the FLIRT DOF by editing the eddy_correct script - though
that would limit the possible corrections of eddy currents.
Cheers, Steve.
On 30 Apr 2008, at 17:58, Herve Lemaitre wrote:
> Hi FSL list,
>
> We are applying eddy_correct to a banch of DTI data. We realized
> that for
> some subjects we got more misregistration between volumes after this
> step.
> We were wondering if it was not due to the fact we are using a b0
> image as
> reference image. The b0 image contains more signal in the skull, the
> eyes
> and the CSF as compared to the weighted images. So, the differences
> between
> these images could drive the registration badly. Should it not be
> better to
> use a weighted image to do this step?
>
> Thanks for your help,
>
> Herve Lemaitre
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
|