Hi
you could quantify the difference between the two examplefund2std
matrices using rmsdiff but I'm not sure that this gives you
meaningful information. Is it the case that the runs were acquired
immediately one after another? Then you could also look at the
registration of the two example_funcs to each other.
Wrt your second question I'm not sure what you mean by 'when
combining across runs within each subject'. Is it the case that you
find weird activations after performing a higher level fixed-effects/
mixed-effects analysis that are not part of any of the lower-level
results? It is possible that mis-registration can cause such edge
effects, its therefore important that you always carefully check the
higher-level registration report.
hope this helps
Christian
On 23 Jul 2007, at 22:56, Vinod Venkatraman wrote:
> Hi,
>
> What is the best way to get an estimate of between-run motion when
> running
> analysis in FSL? I understand that FSL performs motion correction
> within run
> (Mcflirt) using the middle volume of the each run as reference. And
> since
> each run is independently registered to the standard space, I
> suppose there
> is no need to do a between-run motion correction as in other packages.
> However, is it possible to still get an estimate of this value? My
> suspicion
> is that this can be inferred by looking at the registration outputs
> (examplefunc2standard.mat) but am not sure what values to exactly use.
>
> Also, is it possible that between-run motion can cause some form of
> mis-registration which could lead to some weird activations on and
> around
> the ventricles, when combining across runs within each subject?
>
> Vinod
____
Christian F. Beckmann
University Research Lecturer
Oxford University Centre for Functional MRI of the Brain (FMRIB)
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
[log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann
tel: +44 1865 222551 fax: +44 1865 222717
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