Dear FSL Mailing List,
I hope you can help a total beginner. I am trying to run a 1x3 ANOVA (I have 3 groups of subjects and I want to check for differences in their functional connectivity for a specific ROI). The three groups are therefore the different levels of the factor "group". Each level has a different number of subjects corresponding to it (70/16/6). Now I am really confused as to how to create a GLM for it. So far, basing on the FEAT manual, I came up with this (Input1&2 representing Group1, 85 and 86 -- Group2 and 91 and 92 -- Group3):
EV1 EV2 EV3
(mean) (B-mn) (C-mn)
Input1 1 -1 -1
Input2 1 -1 -1
...
Input85 1 1 0
Input86 1 1 0
...
Input91 1 0 1
Input92 1 0 1
However, I am also confused by the differences between https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#Experimental_Designs_-_Between_Subject_ANOVA_Models and https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide#ANOVA:_1-factor_4-levels (in the first example we have -1 in the rows corresponding to the reference level but in the second example we have 0 in the rows corresponding to it), so that I am not sure about it. Question1: Is my version correct? Why is there a difference between sources?
For the contrasts and F-tests I came up with this:
EV1 EV2 EV3
C1 0 1 0 (F-Test selected)
C2 0 0 1 (F-Test selected)
Question2: I don't quite understand how to obtain pure cell means (averages for all three groups) as the guide for that also differs between the manuals. How would I model that?
Question3: Would it be correct to run randomise like this:
randomise -i merged_roi.nii.gz -o /my_path/ -d designmat -t design.con -f design. fts -T ?
Thank you so much!!
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