Hi Oded
You can merge the different repetitions prior to eddy correction
(using fslmerge)
then separate them again prior to averaging (using fslroi)
You need to specify the b0 volumes in both the bvals and bvecs file.
It doesn't matter what values you put in the bvecs file for the b0
images, the important thing is that the bvals and bvecs files refer to
the same number of volumes (and in the same order!)
Cheers,
Saad.
On 22 Jan 2009, at 10:37, Oded Cohen wrote:
> Hi,
> I have a questions regarding FDT analysis sequence with few DTI
> repetitions.
> What would be the right procedure to prepare the data for Bedpostx?
>
> I have prepared a separate 4D file for every repetition, but now I
> can not
> figure out how to make the Eddy correction to apply to the same
> reference image.
> I guess that the averaging should take place after the Eddy
> correction step,
> should I use fslmaths for that?
> Yet another question: I assume that putting B0 volume every 10
> volumes of
> B=1000 is OK - do I need to specify the B0 volumes number ( other
> than in
> bvals) to make it works?
>
> Grateful for your help,
> Thanks,
> Oded
>
Saad Jbabdi
Oxford University FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222545 (fax 717)
www.fmrib.ox.ac.uk/~saad
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