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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nkm
April 04, 2022 09:54AM
Replying years later in case anyone else is interested... I had the same question, wanting to understand precisely how t-statistics are computed when using 3dREMLfit. To manually replicate a t-statistic you'll need to construct or estimate the correlation matrix R as described in the (handwritten...) 3dREMLfit notes. This matrix is neither saved in output nor explicitly stored in memory by the solver given its size.

As a test example to understand construction, given sigma, coef, a, and lambda from stats.REML and stats.REMLvar results datasets, a design matrix X, and a vector or matrix C (tested here as a vector, for a single contrast, for a single run, with no censored TRs) which extracts the contrast of interest, I am able to replicate t-statistics with reasonable precision with a Matlab function explicitly forming R:

function T = REML_tStat(a, lam, std, coef, X, C)
dim = size(X,1);
r = zeros(dim,1);
r(1) = 1; r(2) = lam;
for i = 3:dim
r(i) = lam*a.^(i-2);
end
R = toeplitz(r);
T = coef/sqrt(std^2*C*inv(X'*inv(R)*X)*C');
end

I'm not aware of a convenient/straightforward way to generate whole volumes with AFNI functions but do not believe that would be a worthwhile endeavor anyway.

If there are any glaring errors here I would appreciate those being pointed out by AFNI experts.
Subject Author Posted

Calculate 1st-level t statistics for simple contrasts

herrlich10 October 24, 2018 09:01AM

Re: Calculate 1st-level t statistics for simple contrasts

nkm April 04, 2022 09:54AM

Re: Calculate 1st-level t statistics for simple contrasts

ptaylor April 04, 2022 10:02AM

Re: Calculate 1st-level t statistics for simple contrasts

nkm April 04, 2022 10:15AM

Re: Calculate 1st-level t statistics for simple contrasts

ptaylor April 04, 2022 01:51PM