Hi Xiaochu,

I'm sure Tom will have a better clue than me on this matter, but shouldn't your corresponding p-value to t=3.5 be p=0.0005 (one-tailed t-test)? If the extent of the vox map clusters corresponds to p<0.0005, you've got your answer...

Cheers,
Gwenaëlle


--- En date de : Mar 22.4.08, Zhang, Xiaochu (NIH/NIDA) [F] <[log in to unmask]> a écrit :

> De: Zhang, Xiaochu (NIH/NIDA) [F] <[log in to unmask]>
> Objet: Re: [FSL] FWE randomise and paired t-test
> À: [log in to unmask]
> Date: Mardi 22 Avril 2008, 20h45
> Thank you Gwenaelle and Tom!
> 
> Actually, the extent of the clusters at t=3.5 (i.e.,
> “_tstat” files) is same to the extent of the clusters
> remaining significant after doing randomise -c 3.5 (i.e.,
> “_maxc_tstat” files).
> 
> However, the extent of the clusters at p=0.001 (i.e.,
> “_vox_tstat” files) is bigger the extent of the
> clusters remaining significant after doing randomise -c 3.5
> (i.e., “_maxc_tstat” files).
> 
> Now, I guess the value in “_tstat” is not actually
> t-value in paired t-test.
> 
> Is it correct?
> 
>  
> 
> -----Original Message-----
> From: Gwenaëlle DOUAUD [mailto:[log in to unmask]] 
> Sent: 2008年4月22日 12:52
> To: [log in to unmask]
> Subject: Re: [FSL] FWE randomise and paired t-test
> 
>  
> 
> Hi Tom,
> 
>  
> 
> ahem, Steve pointed out some editing problems in my
> previous email.
> 
>  
> 
> So:
> 
>  
> 
> What Xiaochu did: Glm gui + Wizard for paired t-test in 50
> subjects "before" and 50 corresponding subjects
> "after", so 51 EVs, DF 49.
> 
>  
> 
> What the problem is: when looking at the t-map in fslview,
> the extent of the clusters at t=3.5 is BIGGER than the
> extent of the clusters remaining significant after doing
> randomise -c 3.5.
> 
>  
> 
> Hope it makes sense this time!
> 
> Gwenaelle
> 
>  
> 
>  
> 
> --- En date de : Mar 22.4.08, Thomas Nichols
> <[log in to unmask]> a écrit :
> 
>  
> 
> > De: Thomas Nichols <[log in to unmask]>
> 
> > Objet: Re: [FSL] FWE randomise and paired t-test
> 
> > À: [log in to unmask]
> 
> > Date: Mardi 22 Avril 2008, 14h39
> 
> > Dear Xiaochu,
> 
> > 
> 
> > I'm not sure I understand your question.  Voxel
> and
> 
> > cluster inference will
> 
> > give different results, with cluster inference being
> better
> 
> > when the signal
> 
> > is 'clumpy', and voxel-wise being better for
> focal
> 
> > but intense signals.
> 
> > What works well on one dataset may not work well on
> another
> 
> > dataset.
> 
> > 
> 
> > Hope this helps.
> 
> > 
> 
> > -Tom
> 
> > 
> 
> > On Sun, Apr 20, 2008 at 10:10 PM, Zhang, Xiaochu
> (NIH/NIDA)
> 
> > [F] <
> 
> > [log in to unmask]> wrote:
> 
> > 
> 
> > >  Hi FSL experts,
> 
> > >
> 
> > > I did some group t-test with randomise analysis.
> I
> 
> > usually used the
> 
> > > "Cluster-based thresholding corrected for
> 
> > multiple comparisons by using the
> 
> > > null distribution of the max (across the image)
> 
> > cluster size".
> 
> > >
> 
> > > It worked very well. However, recently I did a
> paired
> 
> > t-test analysis in
> 
> > > my new project. I made the parameter files with
> 
> > "Glm" wizard. However, the
> 
> > > multiple comparison correction made me confused.
> I
> 
> > found the t value (i.e.,
> 
> > > "-c" option) I set is not corrected
> any
> 
> > more. The activated clusters I got
> 
> > > looks very very small. For example, If we
> supposed
> 
> > t=3.5 (DF=48) means
> 
> > > p=0.001 in my study and I used "–c
> 3.5"
> 
> > during the analysis, the "maxc"
> 
> > > files show activated clusters are much smaller
> than I
> 
> > found in "vox" files
> 
> > > with p=0.001 threshold. I found similar results
> in a
> 
> > 2X2 ANOVA analysis,
> 
> > > too. Could you please do me a favor and give me
> some
> 
> > idea of it?
> 
> > >
> 
> > >
> 
> > >
> 
> > > Xiaochu Zhang Ph.D
> 
> > >
> 
> > > Visiting Research Fellow
> 
> > >
> 
> > > NIH/NIDA-IRP
> 
> > >
> 
> > > 251 Bayview Blvd
> 
> > >
> 
> > > Suite 200
> 
> > >
> 
> > > Baltimore MD 21224
> 
> > >
> 
> > >
> 
> > >
> 
> > > Tel: 443-740-2619
> 
> > >
> 
> > > Fax: 443-740-2734
> 
> > >
> 
> > >
> 
> > >
> 
> > 
> 
> > 
> 
> > 
> 
> > -- 
> 
> > ____________________________________________
> 
> > Thomas Nichols, PhD
> 
> > Director, Modelling & Genetics
> 
> > GlaxoSmithKline Clinical Imaging Centre
> 
> > 
> 
> > Senior Research Fellow
> 
> > Oxford University FMRIB Centre
> 
>  
> 
> __________________________________________________
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