good question - see the reply that Joe has just sent in for detail on
that.
:)
On Fri, 2 May 2003, Darren Schreiber wrote:
> Sounds like a good idea. What would you recommend with regards to
> thresholding?
>
> Darren
>
>
> On Friday, May 2, 2003, at 12:02 AM, Stephen Smith wrote:
>
> > Hi Darren,
> >
> > For this semi-exploratory analysis I recommend you switch the
> > higher-level
> > stats to "simple mixed effects" to save a lot of time; you can switch
> > back to FLAME for the final analysis.
> >
> > Thanks, Steve.
> >
> >
> >
> > On Thu, 1 May 2003, Darren Schreiber wrote:
> >
> >> I have been running the higher level analysis of my simplest
> >> experiment
> >> now since Sunday morning. It looks like it will still require a few
> >> more days of processing to be finished (I am using an 867MHz G4 with
> >> 512MB Ram.) As I have looked at the initial results for my simple
> >> contrasts (W, B, N,P), I am getting clusters that contain 20,000
> >> voxels. For instance:
> >>
> >> Cluster List
> >>
> >> Cluster Index Voxels P -log10(P) Max Z x
> >> (mm) y (mm) z (mm)
> >> 2 20330 0 48.6 8.06
> >> -30 -92 4
> >> 1 675 0.000699 3.16 5.23
> >> 26 20 26
> >>
> >>
> >> I ran this analysis using the default settings. Clearly, these
> >> results
> >> are not terribly useful for analysis. I ran this using the default
> >> settings -- cluster thresholding, 2.3, .001.
> >>
> >> I am having exactly the opposite problems for the more complex
> >> contrasts (W>B, B>W, N>P, P>N) and am getting no activations.
> >>
> >> Since this first group analysis is just an exploratory run to help me
> >> learn to run FSL, it isn't a big deal that I'm getting these difficult
> >> to manage results. However, I am going to be doing my next analysis
> >> under more time pressure and it is a substantially more complex
> >> experiment.
> >>
> >> How should I go about rethresholding my runs? Especially, since it
> >> appears I am having two opposing problems. With the simple contrasts,
> >> (W, B, N, P) my understanding is that I should be raising the cluster
> >> thresholding, right? But, which of the two numbers should I be
> >> raising
> >> to get interpretable contrasts? Or, should I just switch to
> >> voxel-based clustering? Or, something else?
> >>
> >> Also, what should I do about the more complex contrasts (W>B, B>W,
> >> N>P,
> >> P>N) in order to see some meaningful activations?
> >>
> >> And, is there a way to simultaneously achieve these seemingly opposing
> >> goals? Or, do I rerun the analysis with higher thresholds to get
> >> meaning out of the simple contrasts and lower thresholds with the more
> >> complex contrasts?
> >>
> >> I am not anxious to meander through the parameter space to find
> >> reasonable settings for the threshold values since there is such a
> >> long time requirement for my data to run. So the wisdom of experience
> >> would be especially critical. Also, since I have more pressing time
> >> problems for my next experiment, any advice on thinking about it?
> >>
> >> Should I use the results that I am generating right now as masks for
> >> the next run? Would that make sense as a solution?
> >>
> >> Darren
> >>
> >
> > 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
> >
>
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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