Just to confirm (and help anyone else who may come across this),
the following should work in Matlab to create the correct mask (from my original binary mask):
NewMask = find(BinaryMask);
Now NewMask is a 1x342934 row vector, in which each column contains one entry that indexes the location of the nonzero elements of my BinaryMask.
From a bit of Googling it seems that 1-based means that counting starts
from 1, which seems to be the case here.
Is there a mistake I'm not seeing?
Thanks,
Seán
On 4 December 2013 19:17, Seán Froudist Walsh froudiss@tcd.ie wrote:
Muchas gracias tío, eres un crack!
On 4 December 2013 19:02, jorge luis jbernal0019@yahoo.es wrote:
I see, the problem seems to be that the input *maskvtx *is not a binary mask. It's a typical Freesurfer's surface label, i.e a vector with the locations (1-based vertices) that are going to be included in the analysis. If you want to include all voxels in the analysis then just set it to the empty vector [] :
*stats = lme_mass_fit_vw(X,[1 2],Y,ni,[]);*
Otherwise enter a vector with the indices of the locations that you want to include in the analysis. *Best* *-Jorge*
El Miércoles 4 de diciembre de 2013 13:43, Seán Froudist Walsh < froudiss@tcd.ie> escribió:
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 jbernal0019@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 < froudiss@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.
- 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?
- 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
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