Hi Steve (and Joe),
Joe's approach is great, I'll try that. Thanks for your kind offer of remote
support. The problem however is that we're in a hospital surrounded by 45
firewalls, making remote access a bit of a cumbersome experience. I do not
really see an easy solution here, but I'll keep it in mind.
Maybe I could make the quick remark here that I really enjoy using FSL
daily. Please, keep it up.
Rutger.
-----Original Message-----
From: Stephen Smith [mailto:[log in to unmask]]
Sent: maandag 2 juni 2003 14:19
To: [log in to unmask]
Subject: Re: [FSL] Higher level FEAT: listing local maxima
Joe's right about the reason - sorry - we should fix that! His workaround is
nice.
WRT your Featquery problem, yes that sounds odd, we've not seen that before.
If you would like, we could log in to your system to see if we can pin it
down.
Thanks, Steve.
On Mon, 2 Jun 2003, Joe Devlin wrote:
> Hi Rutger,
>
> >Okay; I used an uncorrected p, so that must be it. So this means that
> >FSL does not list (coordinates of) local maxima if cluster-based
> >thresholding is turned off? If so, is there perhaps another way in
> >which I can extract coords for local maxima, or should I just use a
> >brain-atlas to locate areas of activation (which is probably less
> >accurate)?
>
> I think this behaviour just reflects a local bias here -- most people
> in Oxford use cluster statistics by default and as a result the
> software never got around to implementing the corresponding tables if
> you chose another option. The way I do it, is to simply choose
> cluster stats and then set the uncorrected threshold I want as the
> z-threshold (say 3.1 for p<0.001
> uncorrected) and set the p-threshold to 1.0. A p-value of one will not
> reject any size cluster (ie it can be as small as a single voxel) so
> effectively the only threshold is the height threshold. And as far as
feat
> knows, it's doing cluster stats so it provides the nice table.
>
> Hope this helps.
>
> Joe
>
Stephen M. Smith MA DPhil CEng MIEE
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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