Hi Punit,
Decided to move this to a separate topic: if things stray too far from the original content of a topic it makes it harder for subsequent readers to find. Can always add links to other topics if you think they are related.
I would like to perform one-way ANOVA followed by t-test.
We need to be very careful here up-front before we even get to the matrices. When you say “followed by”, are you referring to a post hoc test to identify source / direction of effect only where the ANOVA assigned statistical significance? Because that can be done, but:
- It involves running the command twice, not once.
- To do it “properly” (at least as far as I can ascertain) requires utilising a software feature that is implemented but not published and not yet part of a tagged MRtrix3 release.
I am not sure if my model is correct or not.
The “model” in terms of combination of design and contrast matrices is fine; there are multiple possible solutions and this is one of them.
However you are currently performing two t-tests, corresponding to the two rows of your contrast matrix. The first tests the hypothesis that group 1 is greater than group 2; the second tests the hypothesis that group 2 is greater than group 3. In neuroimaging-GLM-speak, an ANOVA is achieved using an F-test. You need two additions:
-ftestsoption, where you provide a text file specifying the set of F-tests you wish to perform and how to construct each. In your case the content of that file should simply be “1 1”: A single row for a single F-test, and that F-test incorporates both of the two rows of the contrast matrix.-fonlyoption, since you don’t actually want to perform those two t-tests, you’re only specifying them to facilitate construction of the F-test.
(I’m currently in an argument with myself as to whether this interface should change)
Cheers
Rob