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Ok, Mark! Thanks a lot for your help! Patricia. 2013/1/21 Mark Jenkinson <[log in to unmask]> > Hi, > > That looks right - any pairwise difference will be detected with this > F-test and so it is looking for any departure from the mean, as an ANOVA > would. The randomise call looks correct to me, and will generate results > for both the t-contrasts and the f-contrast. > > All the best, > Mark > > > On 21 Jan 2013, at 14:02, Patricia Pires <[log in to unmask]> wrote: > > Dear Mark, > > following your advice, i have designed the following matrix (attached). > > Now should i have to run randomise. Is this command correct correct?: > > *randomise -i all_FA_skeletonised.nii -m mean_FA_skeleton_mask.nii -o > resultados_TBSS -d matriz.mat -t matriz.con -f matriz.fts -n 5000 --T2 -V* > > Then, if there is any result, would it be from an ANOVA with post-hoc, > right? > > Thank you very much for your help! > > Patricia. > > 2013/1/21 Mark Jenkinson <[log in to unmask]> > >> Dear Patricia, >> >> Just include 1, 3 and 5 only. >> There are other combinations that would be equivalent, but you must >> restrict it to linearly independent contrasts, and 1, 3 and 5 are the >> simplest set of those. Any other contrast you added to them could be >> generated by a linear combination of these three. And so that is why I >> chose these. >> >> All the best, >> Mark >> >> >> >> >> On 21 Jan 2013, at 10:00, Patricia Pires <[log in to unmask]> >> wrote: >> >> Hello Mark, >> >> thank you very much for your answer. I am not very sure what do you mean >> when you say "*include one F-test that consisted of t-contrasts 1, 3 and >> 5." *Does it mean that my contrast are allright but i have to include >> option F-test=1 and mark t contrast 1, 3 and 5? Why only these contrast? >> >> On the other way, should my randomise command be different than: >> >> randomise -i all_FA_skeletonised.nii -m mean_FA_skeleton_mask.nii -o >> resultados_TBSS -d matriz.mat* -t matriz.con* -n 5000 --T2 -V >> >> -t option in randomise should now be -f because of the F-test analysis? >> >> Thank you very much, >> >> Patricia. >> >> >> 2013/1/19 Mark Jenkinson <[log in to unmask]> >> >>> Hi, >>> >>> If you want a single F-test that checks for any differences then it >>> would be sufficient to use your existing t-contrasts and include one F-test >>> that consisted of t-contrasts 1, 3 and 5. >>> >>> All the best, >>> Mark >>> >>> >>> >>> On 17 Jan 2013, at 11:42, SUBSCRIBE FSL Patricia Pires <[log in to unmask]> >>> wrote: >>> >>> > Dear fsl list, >>> > >>> > i have 4 different groups to analize FA index. I performed a Glm >>> matrix: >>> > >>> > /Matrix >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>> > 1.000000e+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 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+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 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+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 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > >>> > And their contrasts: >>> > >>> > /Matrix >>> > 1.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00 >>> > -1.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>> > 1.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00 >>> > -1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 >>> > 1.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00 >>> > -1.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 >>> > 0.000000e+00 0.000000e+00 1.000000e+00 -1.000000e+00 >>> > 0.000000e+00 0.000000e+00 -1.000000e+00 1.000000e+00 >>> > 0.000000e+00 -1.000000e+00 1.000000e+00 0.000000e+00 >>> > 0.000000e+00 1.000000e+00 -1.000000e+00 0.000000e+00 >>> > 0.000000e+00 -1.000000e+00 0.000000e+00 1.000000e+00 >>> > 0.000000e+00 1.000000e+00 0.000000e+00 -1.000000e+00 >>> > >>> > >>> > There are two contrast with significant results when i run randomise: >>> > >>> > randomise -i all_FA_skeletonised.nii -m mean_FA_skeleton_mask.nii -o >>> resultados_TBSS -d matriz.mat -t matriz.con -n 5000 --T2 -V >>> > >>> > However this procedure has been criticized because there is not a >>> previous overall of results and i am wondering if i first have to do a >>> F-tests: >>> > >>> > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide#F-Tests >>> > >>> > I have to do a F-test first? In that case, what will indicate these >>> results: >>> > >>> > - C1: Group A 1 0 0 0 >>> > >>> > (if i found results here, e.g. cluster >>> --in=resultados_FA_mean_FA_skeleton_mask_tfce_corrp_tstat1.nii.gz >>> --thresh=0.95), would this indicating Group A differ from other groups and >>> then i could finally do my first procedure? Or it is not necessary this >>> first F-test analysis? >>> > >>> > Thanks in advance, >>> > >>> > Patricia. >>> >> >> >> > <GlmANOVAMark.png> > > >