Hi - it sounds like you've not setup one of the first-level registrations
correctly - did you maybe select the structural as the standard image for
one or more of the first-level registration setups? If you can put a
compressed tarfile containing the second level .gfeat analysis on a
web/ftp site we can download and have a look for you.
Cheers, Steve.
On Mon, 7 Feb 2005, Eugene Duff wrote:
> I'm running a second-level analysis with fsl 3.1, across a number of
> subjects. The problem is that the first level spatial normalisation is not
> taken up to the second level analysis, and instead results are registered
> onto one of the hi-res t1 images as the main structural images. I believe it
> may be caused by flirt failing, but when I look at the first level
> analyses, the /reg/ directories seem normal, containing the correct
> standard.img and working .mat files. The only unusual thing about the setup
> is that prestats was run separately, and that fsl 3.2 is also installed on
> the system. The same problem seemed to occur with it when i ran a test with it.
>
> It would be appreciated if someone could help me narrow down the problem,
> Thanks
> Eugene
>
--
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe 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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