I'd like to point out that AlphaSim is quite outdated for a couple of years in AFNI. 3dClustSim is way much more efficient and user-friendly although the underlying mechanism remains the same.
If spatial heterogeneity in smoothing size is of concern, smoothing to a uniform kernel size with 3dBlurToFWHM in AFNI might be an option during pre-processing if applicable.
Cheers,
Gang Chen
On Jan 19, 2012, at 12:00 PM, Anderson Winkler wrote:
> 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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>>>
>>
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