Hi Sean
I'm not sure what is going on. Can you please run the simpler univariate analysis at some random locations? Eg. At location 1000 of your mask (assuming you have to random effects for intercept and time):
[stats, st]= lme_fit_FS(X, [1 2], Y(:, mask(1000)), ni);
If your mask is empty then all vertices/voxels are considered in the analysis. So you should instead run
[stats, st] = lme_fit_FS(X, [1 2], Y(:, 1000), ni);
This can help since you will be able to see the likelihood values through iterations until convergence. Also check the value of st. If the algorithm converge then st must be 1 otherwise it must be 0. Also look out for any prompted error. You will be able to see whether there is any problem with your design matrix.
Given that you have a location as large as 337812 it seems that you are not applying lme to a standard surface-based analysis. Is it a VBM analysis? What is the size of your maskand data matrix Y?
Best -Jorge
El Miércoles 4 de diciembre de 2013 5:04, Seán Froudist Walsh froudiss@tcd.ie escribió:
Dear Jorge and FreeSurfers,
I have just been running lme_mass_fit_vw for 6 hours, and I have seen many thousands of messages like the following:
"Location 337813: Convergence at iteration 4. Initial and final likelihoods: 607.8828, 611.1052. Location 337812: Convergence at iteration 4. Initial and final likelihoods: 603.0934, 604.4513." etc....
There was the very occasional message saying the algorithm did not converge at some location, a message I saw only 2 or three times (although I wasn't looking at the matlab window for 6 hours straight, thankfully). I thought, so far, so good.
I came in to work this morning however, and found that it had finished, with the following ugly message waiting for me:
"Algorithm did not converge at 99.9997 percent of the total number of locations. Total elapsed time is 357.4368 minutes."
I have two questions please.
Should I believe this message, even though it seems to contradict what has been printed to the screen while lme_mass_fit_vw was running?
If it really is a problem, what would you recommend I do to remedy it? Set the convergence epsilon to 10^5?
Any help is much appreciated.
Best wishes,
Seán
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