Hi,
This does seem wrong, although the fslview command looks fine.
What values do you see in the *_corrp_tstat1 file? Are they exactly 1.0 or do they vary at all?
You might find it useful to try one of the other multiple comparison correction options in randomise (e.g., -c) and see if that replicates the same/similar results or is quite different. This will help diagnose whether there is anything wrong in the rest of the pipeline.
As for your second question - all the VBM analysis is done in the template space and that corrects for head-size through the registration (rather than by explicitly calculating ICV) but it is corrected, so you don't need to do anything about that.
All the best,
Mark
> On 3 Jan 2017, at 15:51, Amanda Rodrigue <[log in to unmask]> wrote:
>
> 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?
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