Dear Martin
thank you so much for your answer. Actually, I tried to run the script with the parallel toolbox, but I got some errors and I had to run the version without parallel computing.
Anyway, I will run the script till the end and let you know how results look like. The design matrix is really similar to that reported in the example Web page, since I have only one group, in which I want to estimate the effect of time and time x group interaction
Best
Paola
Da: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Per conto di Martin Reuter
Inviato: 14 July 2016 12:12
A: Freesurfer support list
Oggetto: Re: [Freesurfer] problems by running longitudinal mass univariate analysis
Hi Paola,
1 . It really takes a long time, though I think you probably are missing the parallel toolbox, and running this sequentially will be really slow.
2. You need to wait till the end and look at the percent of places where it did not converge. It is normal that it does not converge in some places. Also make sure the design matrix is not (close to) singular, which can happen if you have nearly collinear columns.
Best Martin
On Jul 14, 2016 10:43 AM, Valsasina Paola <valsasina.paola@hsr.it> wrote:
Dear FS experts
I am trying to run the commands for performing the longitudinal mixed effect statistics with the LME Matlab toolbox.
I am following the instructions on the web page; however, I have two questions:
1) when I run the command lme_mass_fit_vw, the script is running for a very long time, after 3 hours the estimation was just at 10% (unfortunately, my laptop is equipped with Windows and is not particularly powerful). I had to stop the script at that point; before restarting it again I would like to be sure: is this behavior normal? Is it correct that lme_mass_fit_vw is running for such a long time?
2) when the script was running, there were several warnings on the Matlab screen, saying that the algorithm was not converging (at most of locations). Is it also normal? How can I check the correctness of my input image? When I open with freeview the “lh.thickness_sm10.mgh” volume, I just see a black screen with valid timeseries values in the minority of voxels (I imagine that these timeseries are concatenated thickness values of my study subjects). Is there another way to better visualize and check a concatenated 4d mgh file? Failure of convergence is referring to empty/zero voxels of this image?
Thank you for any advice on these two topics
Kind regards
Paola
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