Dear Alex,

>I also get some contrasts that show no activation whatsoever. This is
>strange since these are my main contrasts and the task is based on one
>that has already been reported in the literature. This only happens for
>some individuals (I'm just doing single-subject analyses atm), and I was
>wandering whether this was just due to normal variation, or the symptom of
>something more sinister that I'm not aware of?

Just to add to Christian's response... If this is a cognitive task (rather
than primary sensori-motor), the variability between individuals is
typically rather high so not finding "significant" activations in some
individuals is no surprise.  If you don't find the activation you're
expecting the group stats, then it is worth going back and checking the
individuals to determine why.

>On contrasts (and in subjects) where there is activation, the output only
>seems to report results for very large (>100 voxels) clusters, when I can
>see that there are also smaller clusters. Is there anyway to get the z
>values and coordinates of the smaller clusters?

Yes, this is what cluster statistics do.  An activation is considered
significant if its spatial extent is significantly larger than one would
expect by chance.  To reduce the size of the expected clusters, increase
the Z value.  To see more or less everything of potential interest, put the
Z-value at some reasonably lenient level (like 3.1) and set p=1.0.  Now you
have uncorrected p<0.001 values with no extent threshold and you can see
what's there.  This is exactly equivalent to simply loading the zstat image
into fslview and setting the minimum value to 3.1.  In general, I would
recommend that this is always a useful step in getting to know you're data.

Hope this helps.


Joseph T. Devlin, Ph. D.
FMRIB Centre, Dept. of Clinical Neurology
University of Oxford
John Radcliffe Hospital
Headley Way, Headington
Oxford OX3 9DU
Phone: 01865 222 494
Email:  [log in to unmask]