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The F-test is the mean-sums-of-squares of the effect divided by the mean-sums-of-squares of the error. This could be computed at each voxel, but it would be computationally intensive. Rather, matrix algebra allows the computations to be done very quickly through contrast matrices, projection matrices, and residual forming matrices. The source I've used is: http://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2/pdfs/Ch7.pdf Although, this is an spm source. The GLM is the same process is the same. There are slight difference in the steps leading up to the GLM though, which is why the two programs give slightly different values. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Mon, Apr 16, 2012 at 5:07 PM, Daniel Ferreira <[log in to unmask]> wrote: > Dear Donald, > > Thank you very much once again for your helpful explanations about the orthogonality matter. > > Now I fully understand that there is any problem with the non-orthogonality in the way that FSL runs an ANOVA (1 -1 0; 0 1 -1). > > Taken into account that we are asking for an ANOVA from a non-orthogonal pair of contrasts (1 -1 0: 0 1 -1) could you please detail briefly how FSL does in order to achieve and/or correct the orthogonal principle? > > thank you again in advance > > Daniel