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Hello Matthew, The scans are alphabetically titled as: End_subjectA End_subjectB End_subjectC End_subjectD Pre_subjectA Pre_subjectB Pre_subjectC Pre_subjectD which I believe matches my design matrix. You are right, randomise is still executing but with no further output for hours! Chris On Fri, Sep 24, 2010 at 5:50 AM, Matthew Webster <[log in to unmask]>wrote: > Hello, > This error usually comes from a problem with the design ( such > as mismatch between it and the data ). Can you check that the order of the > scans in your input data matches the order specified in the design? Also is > the randomise process actually terminating after the "integral steps" > message or is it still executing ( it should continue the integration, > although no further output will be written to the screen )? > > Many Regards > > Matthew > > > Hello friends of FSL, > > I am trying to run a pairwise analysis of effect over an intervention, > using 4 subjects, each with one scan before intervention and one scan after > intervention. However, randomise is quitting after 5 permutations with the > "large number of integral steps" error below. This is FSL 4.1.6. Is there > an error in my design matrix? (Made with Glm). It is only a problem with > using the --T2 option. > > Thank you, > Chris Chapman > University of Michigan Medical School > ----- > randomise options: -i all_FA_skeletonised -o TBSS_PAIRWISE -d pairwise.mat > -t pairwise.con -m mean_FA_skeleton_mask --T2 -V --debug > Loading Data: > Data loaded > Confounds detected. > Subject | Design | group | label > 1.000000 1.000000 1.000000 1.000000 > 2.000000 1.000000 1.000000 1.000000 > 3.000000 1.000000 1.000000 1.000000 > 4.000000 1.000000 1.000000 1.000000 > 5.000000 -1.000000 1.000000 2.000000 > 6.000000 -1.000000 1.000000 2.000000 > 7.000000 -1.000000 1.000000 2.000000 > 8.000000 -1.000000 1.000000 2.000000 > > 70 permutations required for exhaustive test of t-test 1 > Input Design: > 1.000000 -1.000000 0.000000 0.000000 0.000000 > 1.000000 0.000000 -1.000000 0.000000 0.000000 > 1.000000 0.000000 0.000000 -1.000000 0.000000 > 1.000000 0.000000 0.000000 0.000000 -1.000000 > -1.000000 -1.000000 -0.000000 -0.000000 -0.000000 > -1.000000 -0.000000 -1.000000 -0.000000 -0.000000 > -1.000000 -0.000000 -0.000000 -1.000000 -0.000000 > -1.000000 -0.000000 -0.000000 -0.000000 -1.000000 > > Input Contrast: > 1.000000 0.000000 0.000000 0.000000 0.000000 > > Contrast rank: 1 > Dof: 3 original dof: 3 > Doing all 70 unique permutations > Starting permutation 1 (Unpermuted data) > statistic Maximum: 49.67 > Starting permutation 2 > statistic Maximum: 1.73205 > Starting permutation 3 > statistic Maximum: 28.6022 > Starting permutation 4 > statistic Maximum: 2.99991 > Starting permutation 5 > statistic Maximum: 9.41493e+14 > Warning: tfce has detected a large number of integral steps. This operation > may require a great deal of time to complete. > > ----- > > view pairwise.mat > /NumWaves 5 > /NumPoints 8 > /PPheights 2.000000e+00 1.000000e+00 1.000000e+00 > 1.000000e+00 1.000000e+00 > > /Matrix > 1.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 > 0.000000e+00 > 1.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 > -1.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 > 0.000000e+00 > -1.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 > -1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 > -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 > > ----- > > view pairwise.con > /ContrastName1 "A > B" > /ContrastName2 "B > A" > /NumWaves 5 > /NumContrasts 2 > /PPheights 2.000000e+00 2.000000e+00 > /RequiredEffect 124.604 124.604 > > /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 > > > -- > Christopher H. Chapman > [log in to unmask] > [log in to unmask] > > > -- Christopher H. Chapman [log in to unmask] [log in to unmask]