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Steve, Thanks for the reply. I am pretty sure I am using the newest version. I am using Randomise version 2.1 which came with FSL version 4.1. Please let me know if there is a newer version of FSL out there that I do not know about. Thanks. Lindsay. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Steve Smith Sent: Wednesday, August 26, 2009 1:34 AM To: [log in to unmask] Subject: Re: [FSL] Randomise TFCE paired t-test biased results? Hi - the first thing I would do is install the latest version of FSL - you are using quite an old randomise, and the way that multiple covariates are handled has improved over various versions. You won't need to change any of the preprocessing - just install the latest FSL and use the version of randomise in that. Cheers. On 25 Aug 2009, at 19:37, Lindsay Walker wrote: > I am using Randomise with the TFCE function (using version Randomise > version > 2.1) to do a paired t-test, where my two groups are the same set of > subjects > processed in two different ways. We want to see the voxel wise > differences > between these two processing methods. I am running this on whole > brain > anisotropy maps which have been scaled to values between 0 and > 1000. I > used the -T option for TFCE, not the --T2, as I am interested in whole > brain, and did not run TBSS on my data. I can provide my design > matrix if > that might help explain things. > > The results are somewhat concerning, in that it appears that > Randomise is > picking up on negative differences, but not positive differences. > In other > words, there are significant differences in the tfce_corrp_tstat2 > file, but > none in the tfce_corrp_tstat1 file. While qualitatively in our data > we see > some positive and some negative differences. We are, therefore, > concerned > that the results are biased in some way. > > Has anyone else experienced anything like this? > > Lindsay Walker. > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------