Hi Amanda,
To add to MJ's answer, I suspect indeed that what you're looking at is a contrast that has no meaning - well, unless your question is: where has my group got GM!
You need to look at your design.mat, and more particularly at your design.con, as this latter will tell you which contrast you are viewing (line 1 corresponds to *_tstat1*). It is likely that you used the GUI to create those files, and by default it creates some (meaningless) contrasts when it comes to structural analyses (VBM, TBSS, ...), whereby you'll see something like, if you have two groups: 1 0. This means: where is there some GM in my first group? (answer: everywhere in the GM!).
Presumably, what you want to ask is: 1 -1: where does group 2 has less GM than in group 1?, or vice-versa. This contrast is (again presumably) further down the line in your design.con, you just need to look at the corresponding *tfce_corrp_tstat?.nii.gz
Hope this helps,
Gwenaëlle
Hello, I'm new to FSL and VBM. I've run through the entire pipeline with no problem but I'm having some issues displaying results. I have three groups that I am trying to compare. I ran the TFCE based option and got the files I was supposed to (I think), but when I use the command provided (fslview $FSLDIR/data/standard/MNI152_T1_2mm GM_mod_merg_s4_tfce_corrp_tstat1 -l Red-Yellow -b 0.949,1) what I see in fslview is essentially all gray matter in yellow. Also the intensity values seem to be the same throughout all gray matter (almost like it is a mask rather than a map of stats?). Am I doing something wrong?
Also another question:
Does FSL's VBM analysis make any correction for ICV? If not how might one do something like that?
