Hi Jorge, Thanks a lot for your reply. I will try out everything you have said. Yes, you're right. I've finally got around to trying out your toolbox on my voxel-based data (see http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31564.html ).
My data matrix Y is 357x2122945 (number of scans x number of voxels) and the mask is 1x2122945. I may have misinterpreted how the mask should be input though. In the help for lme_mass_fit_vw it says that the mask should be 1-based. I thought this might have meant making a binary mask, with ones in the voxels to be included, and zeros elsewhere. lme_mass_fit_vw didn't like the format of the mask so I googled the error, and Google seemed to suggest I should be inputting a logical-type file. So I ran logical_mask = logical(Mask); before running lme_mass_fit_vw. There are 342934 non-zero elements in the mask. This is the amount of points that lme_mass_fit_vw ran for. Many thanks, Seán On 4 December 2013 18:22, jorge luis <jbernal0...@yahoo.es> wrote: > *Hi Sean* > > *I'm not sure what is going on. Can you please run the simpler > univariate analysis at some random locations? Eg. At location 1000 of your > mask **(assuming you have to random effects for intercept and time)**:* > > *[**stats, **st]** = lme_fit_FS(X, [1 2], Y**(:, mask(1000))**, ni);* > > *If your mask is empty then all vertices/voxels are considered in the > analysis. So you should instead run * > > *[stats, st] = lme_fit_FS(X, [1 2], Y(:, 1000), ni);* > > *This can help since you will be able to see the likelihood values > through iterations until convergence. Also check the value of **st. **If > the algorithm converge then **st **must be 1 otherwise it must be 0. **Also > look out for any prompted error. You will be able to see whether there is > any problem with your design matrix. * > > *Given that you have a location as large as 337812 it se**e**ms that you > are not applying lme to a standard surface-based analysis. Is it a VBM > analysis? What is the size of your **mask** and data matrix **Y**?* > > *Best* > *-Jorge* > > > El Miércoles 4 de diciembre de 2013 5:04, Seán Froudist Walsh < > froud...@tcd.ie> escribió: > > Dear Jorge and FreeSurfers, > > I have just been running lme_mass_fit_vw for 6 hours, and I have seen many > thousands of messages like the following: > > "Location 337813: Convergence at iteration 4. Initial and final > likelihoods: 607.8828, 611.1052. > Location 337812: Convergence at iteration 4. Initial and final > likelihoods: 603.0934, 604.4513." > etc.... > > There was the very occasional message saying the algorithm did not > converge at some location, a message I saw only 2 or three times (although > I wasn't looking at the matlab window for 6 hours straight, thankfully). > I thought, so far, so good. > > I came in to work this morning however, and found that it had finished, > with the following ugly message waiting for me: > > "Algorithm did not converge at 99.9997 percent of the total number of > locations. > Total elapsed time is 357.4368 minutes." > > I have two questions please. > > 1) Should I believe this message, even though it seems to contradict what > has been printed to the screen while lme_mass_fit_vw was running? > > 2) If it really is a problem, what would you recommend I do to remedy it? > Set the convergence epsilon to 10^5? > > Any help is much appreciated. > > Best wishes, > > Seán > > _______________________________________________ > 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. > > >
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