Hi Tom,
if I understand correctly, I think that Xiaochu means that, after using the Glm gui and set up the design.mat to be a paired t-test between 50 subjects "before" and the same 50 subjects "after", the problem is that the *extent* of the clusters that remain significant after cluster-based correction should used with the -c option in randomise and this is NOT the case... But I have no clue as for why...
Hope this helps,
Gwenaelle
--- 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, 16h13
> Thank you for your response, Tom!
>
> I’m sorry for my poor English. I tried to make the
> question more clearly.
>
> I’m doing two projects currently. One have 100 subjects
> (50 controls and 50 patients). The randomise result is OK.
> The Cluster-based thresholding corrected for multiple
> comparisons result (i.e., -maxc file) is ok as well.
>
> The other project have only 50 patients but one subject
> have two conditions. I want to compare these two
> conditions. Therefore, I need do a paired t-test. I made
> the “design” files with “Glm wizard”. I think it
> should be corrected. The randomise result (i.e.,
> “_vox_tstat”) looks like ok. However, the dataset
> include t value (i.e..”_tstat” files) is not
> consistent. For example, in my case, if t=3.5 (DF=49),
> p=0.001. However, If I set threshold=3.5 in the
> “_tstat” file and set threshold=0.999 in
> “_vox_stat” file, I found much more and bigger activate
> clusters in the latter. It confused me very much. I knew
> there is something wrong. Could you please help me? Thanks
> a lot!
>
>
>
> ________________________________
>
> From: Thomas Nichols [mailto:[log in to unmask]]
> Sent: 2008年4月22日 8:40
> To: [log in to unmask]
> Subject: Re: [FSL] FWE randomise and paired t-test
>
>
>
> 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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