Hi Jiansong,
Just commenting a bit more:
- About smoothness: It's possible to compute the smoothness using
another AFNI tool, see the command 3dFWHMx.
- About cluster-level FWER, you can still obtain the distribution of the
max cluster size from AlphaSim: see the Max Freq column in the output table.
Thanks to Tom Nichols for pointing this out!
Hope this helps!
Anderson
On 11/01/12 00:28, Anderson Winkler wrote:
> Hi Jiansong,
>
> It isn't generally a good idea to surf different methods until you
> find one in which some results are found. As for AlphaSim you may want
> to know that:
> - It uses Monte Carlo simulations, which is not the same as
> non-parametric methods as it may sound at first. The assumptions of
> parametric methods are all there, and so, there may not be a clear
> advantage over the Random Rield Theory used in SPM. And with RFT, you
> can have t and F statistics too, not just Gaussian.
> - It computes p-values for the clusters individually on the basis of
> their sizes, but there is no FWE correction at the cluster level. This
> requires the distribution of the maximum cluster size under the null,
> which SPM computes parametrically.
> - If you are doing VBM, there is spatial structure (non-stationarity)
> on the statistical map, which you probably would like to take into
> account (see Hayasaka et al (2004) on Neuroimage and the related
> toolbox available for SPM). In AlphaSim, on the other hand, the map is
> assumed to be stationary.
> - AlphaSim doesn't estimate smoothness of the map, which SPM does
> using the residuals of the GLM. This is not quite the same as the
> external smoothing applied during the preprocessing, and the
> difference has a substantial impact on the inference at the end.
>
> Having said this, it is fine to use AlphaSim if none of these issues
> are relevant to your project. Otherwise, I'd probably stick with SPM.
> I can't remember the difference between the correction in SPM2 and
> SPM5 (if I ever knew). In any case, if you have the choice of using
> different SPM versions, I'd suggest to stick with the most recent
> throughout the whole analysis: SPM8.
>
> Hope this helps!
>
> All the best,
>
> Anderson
>
>
> On 09/01/12 18:37, Jiansong Xu wrote:
>> Dear All:
>>
>> I have two questions.
>>
>> 1. Are there any difference in algorithms used for corrections for
>> multiple comparisons between SPM5 and SPM2? My impression is that
>> SPM5 is more restrict than SPM2. For example, if I used height
>> threshold p< .01, a cluster of 100 voxels usually can survive
>> correction in SPM2, but SPM5 needs about 250 voxels.
>>
>> 2. Is it reasonable to use AlphaSim from AFNI to decide cluster size?
>> I noticed that AlphaSim needs much smaller clusters to survive
>> correction relative to SPM5.
>>
>> Best Regards
>>
>> Jiansong
>>
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>> ===============
>> Jiansong Xu, M.D., Ph.D.
>> Assistant Professor
>> Dept. of Psychiatry
>> Yale Medical School
>> 1 Church St., Room 729
>> New Haven, CT 06519
>> Tel: 203-785-5306
>> Fax: 203-737-3591
>>
>>
>
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