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Presumably if you aren't sending this to an SGE cluster, using randomise_parallel is slowing things down, as randomise has to keep stopping and starting and reloading the data….. On 7 Oct 2011, at 17:24, Yingying Wang wrote: > Dear FSL team, > > Is there anything wrong with my settings? I let randomise to run overnight and it is still running after 10 hours. The details are as follows: > > randomise_parallel -i all_FA_skeletonised -o FA_tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -f design.fts -e design.grp --T2 -V > > After this command, I got this message: > Generating 63 fragments of 80 permutation per contrast. Allocating 20 minutes per fragment. > The total number of permutations per contrast will be 5040. > > Then screen is not changing any more after this output mesage. > > The details about all my parameters are here: > > 2 factor (gender and age), each with two level. > > design.mat (four column, gender,age,interaction,EV4): > /NumWaves 4 > /NumPoints 32 > /PPheights 2.000000e+00 2.000000e+00 2.000000e+00 1.000000e+00 > > /Matrix > -1.000000e+00 -1.000000e+00 1.000000e+00 1.000000e+00 > -1.000000e+00 -1.000000e+00 1.000000e+00 1.000000e+00 > 1.000000e+00 -1.000000e+00 -1.000000e+00 1.000000e+00 > 1.000000e+00 -1.000000e+00 -1.000000e+00 1.000000e+00 > 1.000000e+00 -1.000000e+00 -1.000000e+00 1.000000e+00 > 1.000000e+00 -1.000000e+00 -1.000000e+00 1.000000e+00 > -1.000000e+00 -1.000000e+00 1.000000e+00 1.000000e+00 > -1.000000e+00 -1.000000e+00 1.000000e+00 1.000000e+00 > -1.000000e+00 -1.000000e+00 1.000000e+00 1.000000e+00 > -1.000000e+00 -1.000000e+00 1.000000e+00 1.000000e+00 > -1.000000e+00 -1.000000e+00 1.000000e+00 1.000000e+00 > -1.000000e+00 -1.000000e+00 1.000000e+00 1.000000e+00 > 1.000000e+00 -1.000000e+00 -1.000000e+00 1.000000e+00 > 1.000000e+00 -1.000000e+00 -1.000000e+00 1.000000e+00 > 1.000000e+00 -1.000000e+00 -1.000000e+00 1.000000e+00 > 1.000000e+00 -1.000000e+00 -1.000000e+00 1.000000e+00 > -1.000000e+00 1.000000e+00 -1.000000e+00 1.000000e+00 > -1.000000e+00 1.000000e+00 -1.000000e+00 1.000000e+00 > 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 > 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 > 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 > 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 > -1.000000e+00 1.000000e+00 -1.000000e+00 1.000000e+00 > -1.000000e+00 1.000000e+00 -1.000000e+00 1.000000e+00 > -1.000000e+00 1.000000e+00 -1.000000e+00 1.000000e+00 > -1.000000e+00 1.000000e+00 -1.000000e+00 1.000000e+00 > -1.000000e+00 1.000000e+00 -1.000000e+00 1.000000e+00 > -1.000000e+00 1.000000e+00 -1.000000e+00 1.000000e+00 > 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 > 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 > 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 > 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 > > design.con: > /ContrastName1 "gender" > /ContrastName2 "age" > /ContrastName3 "interact" > /NumWaves 4 > /NumContrasts 3 > /PPheights 2.000000e+00 2.000000e+00 2.000000e+00 > /RequiredEffect 1.644 1.644 1.644 > > /Matrix > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 > > design.fts > /NumWaves 3 > /NumContrasts 3 > > /Matrix > 1 0 0 > 0 1 0 > 0 0 1 > > design.grp (16 subjects in total [8 boys v.s. 8 girls],two year data points - set up .grp parameter in order to limit randomization within subject - paired): > /NumWaves 1 > /NumPoints 32 > > /Matrix > 1 > 2 > 3 > 4 > 5 > 6 > 7 > 8 > 9 > 10 > 11 > 12 > 13 > 14 > 15 > 16 > 1 > 2 > 3 > 4 > 5 > 6 > 7 > 8 > 9 > 10 > 11 > 12 > 13 > 14 > 15 > 16 > Thanks a lot. > Yingying --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------