Hi Philipp, thanks for sending the data.
siena_flirt ran perfectly for me. I'm guessing that the problem is
that you're using an old version of FLIRT - some time back there was
a bug when any of the voxel dimensions was <0.5mm, which is the case
here in-plane. The current release works fine.
Note also that the top 2 or 3 slices are corrupted - the intensities
are quite different from the rest of the image - also, in general it
would probably be better to have thinner slices (6mm is rather
thick), even if that means getting worse resolution in-plane.
Cheers, Steve.
On 5 Aug 2006, at 20:44, Philipp Saemann wrote:
> Hello Steve,
>
> we are using siena again to measure atrophy in MS patients from
> clinical T2wi,
> and have some difficulty with the coreg.
>
> We have optimised masks from another study for all baseline/
> followup images,
> as BET was problematic in some cases,
> which extend the brain edge by some 1-2 mm, and also have the other
> three
> images ready (full image, extracted brain, skull image).
>
> We then just skip the two BET lines in SIENA & siena runs through
> successfully,
> but the coreg does not seem to work. I checked the headers of the
> each four starting images, they seem to correspond.
>
> Are there any other prerequisites for coreg? Must the (ANALYZE)
> headers contain some anatomically specific
> origin information?
>
> Thanks for any help,
> many greeting,
> Philipp
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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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