Q: Hi, I am using a simple glim file which contains filename,group but my group has three categories (group1,group2,group3).
After running y~group here:
vs ← mni.vertex.statistics(gf, ‘y ~ group’, vertex.table=dt)
I look at the vertstats file and I have the following tstatistics:
tstatistic.group1
tstatistic.group2\\ tstatistic.intercept
What do these mean though? ie
Does tstatistic.group1 =
group1 vs (group2+group3) ?
group1 vs group2 ?
group1 vs group3?
Is there a way to control the comparisons, or do i have to make separate glim files with a max of two groups in them?

Ideally I would like to see
group1 vs group 2
group1 vs group 3
group 1 vs group2+group3
http://www.bic.mni.mcgill.ca/pipermail/minc-users/2008-November/002263.html

A: Hi, Whenever you run a regression using a categorical predictor, one of the levels of that predictor is designated as the reference level; all other groups are compared against that reference. So, I would suggest:

(1) use the “relevel” command to make sure that the reference group is the one that you want.
(2) as we are using R and not a lesser stats package such as SPSS, I suggest that you explicitly label your levels. See the “levels” and “labels” arguments of the”factor” command. This will make is easier to see what your levels are on your output.
(3) you can, of course, run an analysis using one level as the reference, relevel, and then run again using the new reference, if that’s useful to you.