Hi - I'm not sure exactly what you're doing I'm afraid, but if you
are wanting to end up with everything in the same space I would
recommend using mcflirt on each run separately, and FLIRT to derive
and apply the transforms between the spaces (you can apply flirt to a
4D file).
Cheers, Steve.
On 15 Aug 2007, at 08:26, Satrajit Ghosh wrote:
> I'm trying to run mcflirt on 4 functional runs of a subject and I'm
> trying to realign them to the first volume of the first run using FSL
> 3.3.11
>
> mcflirt -in run1 -refvol 0
>
> mcflirt -in run2 -reffile run1_mcf_meanvol
>
> However, when I load the meanvol (or the mcf files) written by mcflirt
> from run1 and run2 they have different orientation matrices (similar
> but different). I would like these to be identical.
>
> Any help would be much appreciated.
>
> Thanks,
>
> Satra
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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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