Hi,
On 14 Sep 2007, at 14:44, Ed Roberts wrote:
> Hi,
>
> I'm doing the preprocessing steps for an FA analysis and I just wanted
> to check I've got the correct pipeline. My scans have 12 directions
> with 4
> repeats.
>
> Am I right in thinking that if I make these into a 4D file with the
> appropriate bvecs, eddy_correct and dti fit won't have any problems
> with the
> repeated directions? I've tried this and it looks ok.
Yes, this is fine.
>
> Or, should I align the images with eddy_correct, and then average
> them to
> get a 4D file with only 13 volumes? If I do this, presumably I'll
> need to
> alter the bvecs/bvals files?
>
> Also, with regards to the nodif file; should I align the images
> first, then
> fslsplit the 4 x b0 repeats and average them to make the nodif?
You can if you wish - see recent posts on this - it _might_ be worth
the extra hassle, but the gain is likely to be minimal.
Cheers.
>
> cheers,
>
> ed
>
> p.s. thanks for organising the course in Cardiff, very useful.
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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
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