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
>
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