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Hey Darren - Whether you can split up the second level copes, depends on the design. In general, it's not a good idea. However you _can_ split up the first level copes so, in your case, you can run 9 times faster ( a single .gfeat for each first level cope ) and all should be good. You can also spread out the load spatially. At the flame stage (before Random fields/clusters etc.) everything is done voxel-by-voxel, so you can split them as much as you want and then merge them at the end before doing thresholding. I don't believe there is any multi-threaded code in FSL3.0 or 3.1 so I don't think any multi-processor stuff wil happen without you doing it yourself! wrt using stage-1 only. The "party line" advice is to use stage-1 to check things out, but to use the total flame when you're publishing. Just depends on how patient you're feeling I guess. I think the results will be pretty similar... Hope this helps T ------------------------------------------------------------------------------- Tim Behrens Centre for Functional MRI of the Brain The John Radcliffe Hospital Headley Way Oxford OX3 9DU Oxford University Work 01865 222782 Mobile 07980 884537 ------------------------------------------------------------------------------- On Tue, 2 Mar 2004, Darren Schreiber wrote: > I am using FSL 3.0 to conduct a second level analysis of my "pictures > experiment" data. I have nine contrasts done on the first level and > twelve contrasts on the second level. Generating one cope1.gfeat > directory on the second level is taking about 24 hours of processing. > So, doing the whole analysis looks like it should take about nine days > (we are on day 3 now.) > > I am going to be doing the second level analysis of my "faces" data > later this week and was thinking of ways to speed it up. Since I am > running processes on a clustered machine, I was thinking that I could > generate twelve .fsf files to represent each of my second level > contrasts separately. Then I was thinking that I could run them all in > parallel and reduce the processing time to 24 hours or less total. Is > there anything that would prevent me from running multiple, parallel > second level contrasts? > > I'm also going to see if we can get FSL 3.1 on this machine. I vaguely > recall that 3.1 might have the capacity to split up processes into > threads that could be done in parallel automatically? Is that right? > > And, I was thinking of using just the 1st stage FLAME in FSL 3.1 due to > the speed up and small accuracy sacrifice. Is my thinking here good? > > As always, thanks for the help with this. > > Darren >