Hi Laura,

it is perfectly plausible that you don't get any significant result, especially after correction for multiple comparisons. Look at your uncorrected p-values or t-values maps to have an idea of the pattern of possible abnormalities (see randomise manual).
The number of permutations is based on the number of subjects you've entered in your model. With only 6 subjects, you won't need 5000 permutations.

Cheers,
Gwenaelle


--- En date de : Mar 30.9.08, Laura D <[log in to unmask]> a écrit :

> De: Laura D <[log in to unmask]>
> Objet: [FSL] no significant clusters!
> À: [log in to unmask]
> Date: Mardi 30 Septembre 2008, 16h42

> Hi all--
>
> I'm just learning to use FSL, and this forum's been
> very helpful in
> answering all my questions when things go wrong or the
> instructions are
> incomplete. However, I've run into something there
> aren't any answers for so
> far: I'm getting no significant clusters, even when my
> 1-p is set all the
> way to .4!
>
> All files have been generated properly, everything's
> been smooth. Admittedly
> I've only used 3 controls and 3 patients, as I wanted
> things to run quickly.
> Still, there ought to be something at p = .6! Here're
> the two randomise
> commands I ran (I tried s=2,3,4, all with nothing), per the
> "Running FSL-VBM
> (Detail)" displaying results step:
>
> randomise -i GM_mod_merg_s3 -m GM_mask -o fslvbm -d
> design.mat -t design.con
> -T -n 5000 –V
>
> fslview $FSLDIR/data/standard/MNI152_T1_2mm
> fslvbm_tfce_corrp_tstat1 -l
> Red-Yellow -b 0.4,1
>
> One thing I also found curious was that apparently only 20
> permutations were
> run with the first command, although I specify 5000. Is
> that normal?
>
> Thanks!