Dear Martin
to follow-up mu previous question, I was finally able to run the lme_mass_fit_vw script till the end. Unfortunately, it came out that converge
of the algorithm was failed in 99% of the locations.
I have only one study group (with a variable number of follow-up , and I used as design matrix exactly the same proposed in the online guide:
X=[ones(length(M),1) M M(:,1).*M(:,2)]
so, I don’t see any specific region of failure associated with the design matrix
Therefore, I suppose that this is due to the fact that input images are wrong (empty or with some problems?).
How can I investigate further the correctness of my input data? The longitudinal pipeline was performed correctly, and mris_preproc command to
generate the mass univariate file seems to work without errors. Can I eventually load somewhere my image file (i.e., the concatenated lh.thickness.mgh including all scans), so that someone chan check that input images for lme estimation are OK?
Thank you so much in advance
Kind regards
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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