Hi Eric

One way to check your design matrix and data for posible errors is by performing a simple univariate analysis using data from a single vertex, eg. at vertex 1000:

lhstats = lme_fit_FS(X,Zcols,Y(:,lhcortex(1000)),ni);

and check the behavior of the optimization procedure. Make sure that both your design matrix X and the cortical thickness data   Y are ordered in a way that they contain all the repeated measures for the first subject (ordered by time), then all the repeated measures for the second subject and so on. The first element of the vector ni must indicate the number of repeated measures in the design matrix X for the first subject, the second element of that vector must indicate the number of repeated measures in the design matrix for the second subject and so on.

Take a look at the header of lme_mass_vw script for the size of the X, Y etc...

Best -Jorge

El Lunes 17 de marzo de 2014 18:35, Eric Cunningham etc42@hawaii.edu escribió:

Hello Freesurfer experts,

The lme_mass_vw script runs for a long time and outputs info into the matlab terminal.  Most look like this:

Location #####: Algorithm did not converge.  Initial and final likelihoods: ###, ###

Running this script, for almost every line, the initial and final likelihoods are "Inf".  Is this indicative of a problem?

Getting these results made me wonder if the Y-input was built 

properly.  Using mris_preproc and mri_surf2surf to smooth, we tested 10mm smoothing and no smoothing in addition to the 30mm smoothing we had been doing originally.  The results:

smoothed to 30 ~ almost every likelihood = Inf, Inf

smoothed to 10 ~ some (1 in 5? 10?) likelihood = Inf

not smoothed ~ no instances of likelihood = Inf, Inf

Thanks, -Eric _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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