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Hi Aisha, hi Brigitte, That's more clear, thank you. For the structural analysis the design would indeed use a paired t-test. You could also compute the difference between after and before treatment and use that in a one-sample t-test. The follow up analysis using would use the differences (computed as in the option above) in FA vs differences in the behavioural measurement. The design could also be akin to the paired t-test, with the additional variable included for testing. However, if there are differences in the behavioural measurements over time, this the whole analysis will fall into the "voodoo" category, that is, it becomes a circular, invalid analysis. To make this more clear, you must not correlate a set of quantities A (like FA) and a variable B (like time), then take the best correlations in A and correlate these with C (like the behavioural measurements), when C is not independent of B. All the best, Anderson On Wed, 14 Nov 2018 at 07:01, Dr A.B.C. Dijkshoorn <[log in to unmask]> wrote: > Dear Andersson, > > Thank you very much for your response. > > With the structural analysis I mean whether we can observe a change in > FA before-after intervention. > With the structural-behavioral analysis I mean whether the change in FA > (before-after intervention) is correlated to change in performance on a > cognition test. > > > In essence, are the paired t-test design matrixes different in the > structural analysis (10 EVs, eye-shaped design matrix) from the > structural - cognition analysis (put cognition data in 1EV column or use > the eye-shaped design matrix?) > > Does this clarify your question? > > Best wishes, > Aicha > > > > On 2018-11-14 11:47, Anderson M. Winkler wrote: > > Hi Brigitte, > > > > I don't really understand what you mean by "struct-behav" analysis and > > how that would differ from the "struct" analysis. Also I don't > > understand what you mean by the "this" in your first paragraph (see > > highlighted below). Could you clarify? > > > > Thanks! > > > > All the best, > > > > Anderson > > > > On Thu, 8 Nov 2018 at 07:13, Brigitte Evers <[log in to unmask]> wrote: > > > >> Dear FSLusers, > >> > >> I am fairly new to TBSS and would like to check if I am doing the > >> correct thing! I am trying to do a paired t-test to look at > >> structural changes in FA before and after an intervention in 9 > >> lesion patients. I then want to correlate THIS to performance on an > >> cognition task. I am aware that I have 2 options (1) subtracting FA > >> images post-intervention from pre-intervention with fslmaths (2) > >> create design and contrast files according to FEAT paired t-test > >> manual (we chose for the latter for visualisation purposes) > >> > >> My question is do I set up the struct-behav analysis matrix file > >> the same as the structural analysis part (e.g. 10 EVs/columns) or do > >> I just create 1 EV/column with cognition data (+additional columns > >> for covariates) with the struct-behav analysis (and how do I know > >> FSL "remembers" the within subjects group design of the structural > >> part)? > >> > >> Any help you could offer would be highly appreciated! > >> > >> Best wishes, > >> Brigitte > >> > >> For the structural analysis I have created contrast and matrix > >> files according tp the FEAT manual: > >> /NumWaves 10 > >> /NumPoints 18 > >> /PPheights 2.000000e+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 > >> > >> /Matrix > >> /NumWaves 10 > >> /NumPoints 18 > >> /PPheights 2.000000e+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 > >> > >> /Matrix > >> 1.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 0.000000e+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 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 > >> 1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 > >> 0.000000e+00 0.000000e+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 > >> 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 0.000000e+00 > >> 1.000000e+00 0.000000e+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 > >> 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 > >> 0.000000e+00 0.000000e+00 > >> 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+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 0.000000e+00 > >> 0.000000e+00 0.000000e+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 0.000000e+00 0.000000e+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 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 > >> -1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 > >> 0.000000e+00 0.000000e+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 > >> 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 0.000000e+00 > >> -1.000000e+00 0.000000e+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 > >> 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 > >> 0.000000e+00 0.000000e+00 > >> -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+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 0.000000e+00 > >> 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 1.000000e+00 > >> > >> /NumWaves 1 > >> /NumPoints 18 > >> > >> /Matrix > >> 1 > >> 2 > >> 3 > >> 4 > >> 5 > >> 6 > >> 7 > >> 8 > >> 9 > >> 1 > >> 2 > >> 3 > >> 4 > >> 5 > >> 6 > >> 7 > >> 8 > >> 9 > >> > >> /ContrastName1 preint - postint > >> /ContrastName2 postint - preint > >> /NumWaves 10 > >> /NumContrasts 2 > >> /PPheights 2.000000e+00 2.000000e+00 > >> /RequiredEffect 5.446 5.446 > >> > >> /Matrix > >> 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+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 > >> 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> > >> For the functional analysis I am doubting between these 2 contrast > >> matrixes (I used the same .grp file) > >> (1) > >> /NumWaves 1 > >> /NumPoints 18 > >> /PPheights 2.000000e+01 > >> > >> /Matrix > >> 1.900000e+01 > >> 1.800000e+01 > >> 2.000000e+01 > >> 1.700000e+01 > >> 1.900000e+01 > >> 1.900000e+01 > >> 1.800000e+01 > >> 2.000000e+01 > >> 1.600000e+01 > >> 5.000000e+00 > >> 7.000000e+00 > >> 4.000000e+00 > >> 7.000000e+00 > >> 8.000000e+00 > >> 5.000000e+00 > >> 7.000000e+00 > >> 8.000000e+00 > >> 2.000000e+00 > >> > >> (2) > >> /NumWaves 10 > >> /NumPoints 18 > >> /PPheights 2.000000e+00 5.000000e+00 > >> 6.000000e+00 6.000000e+00 6.000000e+00 6.000000e+00 > >> 6.000000e+00 6.000000e+00 6.000000e+00 5.000000e+00 > >> > >> /Matrix > >> 1.000000e+00 5.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 > >> 1.000000e+00 0.000000e+00 6.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 > >> 1.000000e+00 0.000000e+00 0.000000e+00 5.000000e+00 > >> 0.000000e+00 0.000000e+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 > >> 6.000000e+00 0.000000e+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 6.000000e+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 0.000000e+00 6.000000e+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 0.000000e+00 0.000000e+00 6.000000e+00 > >> 0.000000e+00 0.000000e+00 > >> 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 4.000000e+00 0.000000e+00 > >> 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 5.000000e+00 > >> -1.000000e+00 4.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 > >> -1.000000e+00 0.000000e+00 6.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 > >> -1.000000e+00 0.000000e+00 0.000000e+00 6.000000e+00 > >> 0.000000e+00 0.000000e+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 > >> 5.000000e+00 0.000000e+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 6.000000e+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 0.000000e+00 6.000000e+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 0.000000e+00 0.000000e+00 6.000000e+00 > >> 0.000000e+00 0.000000e+00 > >> -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 6.000000e+00 0.000000e+00 > >> -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > >> 0.000000e+00 5.000000e+00 > >> > >> > > ######################################################################## > >> > >> To unsubscribe from the FSL list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 [1] > > > > ------------------------- > > > > To unsubscribe from the FSL list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 [2] > > > > Links: > > ------ > > [1] https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > > [2] https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > > ######################################################################## > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1