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Hey Darren, sounds like u need a new system! I found a new 1Gb 333MHz DDR system with an athlon 1700+ (all on an EPOX mbo) basically doubled the processing speed over a Pentium III 733MHz system with 512Mb RAM. Mind you, if you lack the RAM it will swap out, so you still need a really fast disk and a dedicated partition (4Gb max for 32 bit systems). I'd bet your system is swapping out like crazy. If you can, check the memory page "faults" and i/o. Cheers, Darren ----- Original Message ----- From: "Darren Schreiber" <[log in to unmask]> To: <[log in to unmask]> Sent: Friday, May 02, 2003 3:00 PM Subject: [FSL] Higher Level Analysis Thresholding Wisdom Needed > 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 .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 >