Hi - no, as long as phase encoding is always in the same direction
(it will be) it doesn't matter that your slice ordering is interleaved.
Have you tried doing full unwarping of the FMRI data, and not just
FLIRT cost-function weighting?
You should be able to easily use fslmaths to get a CSF-related
weighting image.
Cheers.
On 10 Oct 2007, at 22:40, Christopher Bell wrote:
> Hello,
>
> Has anyone tried using sigloss with interleaved slice collection?
> So far I
> have calculated the sigloss image, and used the flirt options --
> inweight
> (sigloss output), -searchcost (normcorr) and -cost (normcorr) to
> register
> the fmri image to our PD image. These options are successfully
> moving the
> alignment in the right direction by about 1 mm, but there is still
> about 4mm
> to go. I have tried registering to the T1 as well, but it seems to
> move the
> alignment in the opposite direction! Does anyone know if
> interleaved slice
> collection disrupts the sigloss calculation or have any
> suggestions? Thanks.
>
> Chris Bell
>
> PS: Any suggestions on how to best apply ventricle weighting from
> the fmri
> to a PD or a T1, to achieve better alignment.
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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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