The spatiotemporal lme model is more advanced than the traditional vertex-wise lme but it's also more difficult to setup with the current scripts.
So I'd suggest you simply use the easier traditional vertex-wise lme:1-Read your label eg.: lhcortex = fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');
2-Read the data file eg.:
[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');
3-Fit a vertex-wise lme model with random effects for the intercept and time terms eg.: lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);
4-Perform vertex-wise inference eg.: CM.C = [your contrast matrix]; F_lhstats = lme_mass_F(lhstats, CM);
5-Save results eg.: fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig');
HTH-Jorge
De: David Pagliaccio david.pagliaccio@gmail.com Para: freesurfer@nmr.mgh.harvard.edu Enviado: Jueves 4 de Mayo de 2017 9:04 Asunto: [Freesurfer] lme_mass_RgGrow problem
Hello,We have been trying to analyze some longitudinal structural data using the FreeSurfer Mixed Effects Model toolbox and have been running into some issues. We have 2-3 timepoints per individual imaged across adolescence and 3 groups of interest. We set up a design matrix to examine potential quadratic effects of age by group including factors for:1. Intercept2. time3. time ^24. Group 1 vs. others5. Group 1 x time6. Group 1 x time ^27. Group 2 vs. others 8. Group 2 x time9. Group 2 x time ^210. age at baseline11. sex We started a model to examine thickness, testing out the first model below[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2 3],Y,ni,lhcortex);
Then, we have been getting stuck at [lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere,lhRe,lhTh0,lhcortex,2,95);
This starts the segmentation into homogeneous region but seems to get stuck after displaying "Computing seeds..." Is there a way to diagnose or fix this problem? Any thoughts would be great, thanks!_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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