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. Intercept
2. time
3. time ^2
4. Group 1 vs. others
5. Group 1 x time
6. Group 1 x time ^2
7. Group 2 vs. others 
8. Group 2 x time
9. Group 2 x time ^2
10. age at baseline
11. 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.