Dear FSL-experts,
I am very sorry for bringing up this question again! I am new to FSL and tried reading up on TBSS and contrast settings in F-tests in the mailing list and the tutorials, but got a little confused.
I would like to compare 3 groups of patients (no healthy control group as reference in my design) on their FA values in TBSS. Assuming I have 2 participants in each group, my model looks like this:
Group Group 1 Group 2 Group 3
1 1 0 0
1 1 0 0
1 0 1 0
1 0 1 0
1 0 0 1
1 0 0 1
If I understood the FEAT tutorial correctly, the group column should be all 1’s or is that incorrect and it should rather be:
Group Group 1 Group 2 Group 3
1 1 0 0
1 1 0 0
2 0 1 0
2 0 1 0
3 0 0 1
3 0 0 1
I found both information on the tutorial and am confused as to which one is the right one.
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#F-Tests_.28Inter-Group_differences.2C_no_repeated_measures.29 OR http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide#F-Tests
I would like to run an F-test first and follow up a significant result using pairwise t-tests. Following the tutorial, I set up the following contrasts for the F-test:
contrasts F-test
Group 1 1 0 0 x
Group 2 0 1 0 x
Group 3 0 0 1 x
I would calculate this first and then set up a second analysis with t-contrasts after receiving significant results. Or would it be better to set up the contrasts as follows and have both analyses (F-test and follow up analysis) all in one step:
contrasts F-test
x gr 1>gr2 1 -1 0 x
x gr 1>gr 3 1 0 -1 x
x gr 2>gr1 -1 1 0
x gr 2>gr3 0 1 -1
x gr3>gr1 -1 0 1
x gr3>gr2 0 -1 1
However, in the latter case I am not sure which contrasts to choose as F-tests, since I do not have any control group for which I would assume higher FA values or that I could use as a reference. Would I randomly choose two f-tests?
Any help would be highly appreciated! Thanks!
Bianca Kollmann, PhD candidate
Department for Clinical Psychology and Neuropsychology
Johannes Gutenberg-University Mainz, Germany
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