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Hi You also need to de-mean the confound variable (i.e. remove the mean age in your example from each one of the numbers) - otherwise all correct. hth Christian On 30 Apr 2009, at 19:52, Silviu Podariu wrote: > Hello, > > I am trying to make sure I am doing a 2-group t-test with additional > variables (age and sex are tipical choices) correctly, according to > the instructions at www.fmrib.ox.ac.uk/fsl/randomise/index.html. > > For space/illustration purposes, let's say I have a group A of N_A=3 > subjects, and a group B of N_B=4. The design.mat/con files produced > with > the design_ttest2 tool and used in the randomise command are: > > ==== design.mat with no additional variables: > /NumWaves 2 > /NumPoints 7 > /PPheights 1 1 > /Matrix > 1 0 > 1 0 > 1 0 > 0 1 > 0 1 > 0 1 > 0 1 > ==== design.con : > /NumWaves 2 > /NumContrasts 2 > /PPheights 1 1 > /Matrix > 1 -1 > -1 1 > ==== ==== ==== > > My understanding, should I wish to add an additional (confounding) > variable, like age, is that I should add another column (with > appropriate age values) to the design.mat file, and leave the contrast > file and everything else unchanged (thereby the contrast ignoring the > new variables): > > ==== design.mat with additional -age- variable: > /NumWaves 2 > /NumPoints 7 > /PPheights 1 1 > /Matrix > 1 0 24 > 1 0 48 > 1 0 35 > 0 1 29 > 0 1 47 > 0 1 22 > 0 1 31 > ==== ==== ==== > > and that I should use exactly the same randomise command as before to > compute the tfce_p_tstat images, with the obvious modification should > I wish to include even more (confounding) variables. > > Is this correct? > > Also, when the simple 2-group t-test is done, a number of (N_A + > N_B)!/( N_A! * N_B! ) maximum permutations are possible to choose N_A > subjects for the first group. However, when additional variables are > used, there seems to be room for more shuffling rather than just group > membership. Actually, I ran the randomise command with the -q option > for these design files and I obtained an exhaustive number of > permutations equal to 2520=35*72 in place of the 35 initial ones > (before adding the 3rd column). Is there a simple explanation for this > number (the multiplicative 72 factor)? > > Thank you very much, > Silviu Podariu > UNMC, Omaha _______________________________________________ Christian F. Beckmann, DPhil Senior Lecturer, Clinical Neuroscience Department Division of Neuroscience and Mental Health Imperial College London, Hammersmith Campus Rm 419, Burlington Danes Bldg, Du Cane Road, London W12 0NN, UK Tel.: +44 (0)20 7594 6685 --- Fax: +44 (0)20 7594 6548 Email: [log in to unmask] http://www.imperial.ac.uk/medicine/people/c.beckmann/ Senior Research Fellow, FMRIB Centre University of Oxford JR Hospital - Oxford OX3 9DU Tel.: +44 (0)1865 222551 --- Fax: +44 (0)1865 222717 Email: [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann