AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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January 06, 2010 12:07PM
My take on the matter is that there are good points and bad points to the two approaches (AlphaSim and Smooth Random Field = SRF).

AlphaSim good point: doesn't rely on asymptotic formula for tail probability in the limit of large smoothness. When the smoothness is more than (say) 3-4 voxel dimensions, the asymptotic formula is probably good -- for smaller smoothness, only a simulation approach like AlphaSim can give semi-accurate cluster p-values (IMHO).

AlphaSim murky point: assumes the statistics are equivalent to p-values from a jointly NORMAL random field, whereas that isn't quite true (the statistics are usually from a jointly Student-t distributed field). How much difference this makes is unclear to me. The SRF approach uses asymptotic formula derived by the late lamented Keith Worsley for each case of the underlying distribution -- this issue can be considered a good point for SRF vs. AlphaSim. (Of course, in principal AlphaSim could be modified to use different distributions, but that would be something like work.)

AlphaSim bad point: it is slow and not easily encoded into a formula -- so you can't just set a threshold and get a p-value back right away.

AlphaSim good point: it allows for the actual geometry of the brain mask in its simulations. This is probably a very minor point -- that is, it treats the edge of the brain more correctly, but how much of the brain is at the edge?

The real issue (again, IMHO) is the smoothness point. If one is smoothing the hell out of the data, then the asymptotic formulae used in the SRF method are accurate and much easier to use than AlphaSim. If one is NOT smoothing so much, then AlphaSim should be superior. At the cost of having to run the damn thing for every case, of course.

Subject Author Posted

Alphasim assumptions?

Desmond January 06, 2010 11:41AM

Re: Alphasim assumptions?

bob cox January 06, 2010 12:07PM

Re: Alphasim assumptions?

Gang Chen January 06, 2010 12:15PM

Re: Alphasim assumptions?

Desmond January 07, 2010 12:17PM

Re: Alphasim assumptions?

Gang Chen January 07, 2010 02:12PM