Martin,

Doing the changes in the matrix allowed me to run the command. The command with just one random effect for the intercept term give me the following output:

Aproximate percentage of fitted locations: 100%

Summary:

Algorithm did not converge at 23.407 percent of the total number of locations.

Total elapsed time is 116.2184 minutes.

Is this ok? Is there anything I should check?

Should I also try two random effects as well?

Thank you

Pablo

To: freesurfer@nmr.mgh.harvard.edu
From: mreuter@nmr.mgh.harvard.edu
Date: Tue, 20 Oct 2015 09:06:53 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed} {Disarmed}

Hi Pablo,

the zero columns could be outside the cortex and then this would be fine. Do
min(sum(lhY(:,lhcortex)))
if you get 0 you have at least one location where the column is all zero (as we should not have any negative values, you can test that with min(lhY(:))
Now even if you still have a column of 0 , then that vertex is problematic, but who cares about a single vertex. If you do a region approach, it will be part of a region anyway. so you should check how often you get 0 columns (inside cortex).

About your M: I would subtract 1 from gender (to have 0 and 1)
Also you only need 2 columns for the groups: keep only column 3 and 4. A HC is someone who has 0 in both.

Best, Martin

On 10/20/2015 04:37 AM, pablo najt wrote:

Dear FS experts,
I am following up on an issue I am having when trying to run linear mixed effects model. I keep getting 'Algorithm did not converge'.

So far I have changed the preprocessing steps following literally from the wiki as in message below. Also I tried to use only one random effect for the intercept. Also I have checked that sum of vectors of (ni) is equal to the number of rows in (X).

As none of the above worked I started to have concerns about the dimensions of my lh.thickness_sm10.mgh. When I load in matlab in working space says 'too many variables'. Is this ok?

Also, when I open 'lhY' variable it shows a column of Zeros every nine columns as below. Is this alright?

Perhaps this is fine but I would like to check on anything that is creating this problem. For matrix 'M' I created a matlab script that loads a matrix with intercept (all ones), HC (ones to HC otherwise zero), U_PT (relatives of patients ones otherwise zero), PT (patients one otherwise zero), gender, age (see below). The three columns for groups do not match the qdec.table.dat which have only one column for groups (HC, U_PT, PT). However the order of the rows is identical in M and qdec.table.dat

Please let me know if this should be set differently.

Thank you

Pablo
To: freesurfer@nmr.mgh.harvard.edu
From: mreuter@nmr.mgh.harvard.edu
Date: Mon, 19 Oct 2015 09:00:57 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Hi Pablo,

since you did not run this through the longitudinal stream, you won't have a base ( or subject-template), also you won't have <tpid>.long.<base> directories, so the first command should fail. For that you simply replace the --qdec-long with --qdec and use the same table. Should work. The second command is fine (it just smoothes the thickness stack).

Best, Martin

On 10/19/2015 06:51 AM, pablo najt wrote:
Hi Jorge and FS experts,
I have run again the analysis and still get the convergence problem.

I am assuming the issue has to do with the preprocessing steps, as I had doubts on how to follow from the instructions if I am not using qdec and have a cross sectional design.

Instructions on lme in the wiki for preprocessing specify the following:
mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh
mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex  --noreshape
My data -as I explained below- is cross section but I want to treat it as longitudinal as I want to analyse subjects belonging to the same family.

Here is my 2 main questions:

1) for preprocessing should I follow instructions as it would be longitudinal data?

2) Although my design does not allow using qdec (3 groups) do I still create a qdec table and follow literally the two instructions above ?

Thank you

Pablo
____________________________________________________________________________________________________________________________________
Date: Fri, 16 Oct 2015 16:24:36 +0000
From: jbernal0019@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
CC: pablonajt@hotmail.com
Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
Hi Pablo

Yes, too many locations at which the estimation algorithm didn't converge is problematic. That might mean that having two random effects is not appropriate for your data. You should try to run the command with just a single random effect for the intercept term:

lhstats = lme_mass_fit_vw(X, [1], lhY, ni, lhcortex, [], 4);

If the result still have too many non-convergence locations then something might be wrong with the ordering of the design matrix and its correspondence with the ordering of the ni vector or the ordering of the image data etc... You will need to check it thoroughly.

Cheers

-Jorge
De: pablo najt <pablonajt@hotmail.com>
Para: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Enviado: Viernes 16 de octubre de 2015 1:43
Asunto: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
Thanks you for the replies.
Jorge and FS experts,

I have run the analysis and first double checked that the sum of vectors of (ni) is equal to the number of rows in (X). Both are 140 which is the number of my subjects.

The analysis gave the following 'error'(?) below:

I looked up a previous thread coming across this. At that case you recommended

Would you recommend this afain>

Aproximate percentage of fitted locations: 100%

Warning: matlabpool will be removed in a future release.

To query the size of an already started parallel pool, query the 'NumWorkers'

property of the pool.

To check if a pool is already started use 'isempty(gcp('nocreate'))'.

Warning: matlabpool will be removed in a future release.

To shutdown a parallel pool use 'delete(gcp('nocreate'))' instead.

Parallel pool using the 'local' profile is shutting down.

Summary:

Algorithm did not converge at 90.0637 percent of the total number of locations.

Total elapsed time is 550.1023 minutes.

Also almost all the time the screen showed the following message:

144114: Algorithm did not converge. Initial and final likelihoods: -38.3408-1.5708i, -241.4153-1.570796i.

Location 144113: Algorithm did not converge. Initial and final likelihoods: -5.5424-1.5708i, -133.8004-1.570796i.

Location 144112: Algorithm did not converge. Initial and final likelihoods: -7.7571-1.5708i, -319.1378-1.570796i.

Location 144111: Algorithm did not converge. Initial and final likelihoods: -16.8597-1.5708i, 0.74448.

Aproximate percentage of fitted locations: 100%
So my two questions are:

1. Is this problematic?

2. Are there any fixes to this issue?

Thank you,

Pablo
Date: Thu, 15 Oct 2015 13:38:22 +0000
From: jbernal0019@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
CC: pablonajt@hotmail.com
Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
Hi Pablo

The error you are getting is because in your Matlab setup you can only request a maximum of 4 matlab parallel workers and by default lme requests 8. So you just need to modify your command like this:

lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex, [], 4);

Please make sure that sum(ni) and length(X) give the same value before running the above command.

Cheers

-Jorge
De: pablo najt <pablonajt@hotmail.com>
Para: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Enviado: Jueves 15 de octubre de 2015 7:18
Asunto: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
Thank you Martin.
I am trying to run the following command line and get the error below. Would you have a suggestion to overcome this issue?

Just in case I am also including a snapshot of my loaded variables at the bottom.

Many thanks,

Pablo

>> lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);

Warning: matlabpool will be removed in a future release.

To query the size of an already started parallel pool, query the 'NumWorkers'

property of the pool.

To check if a pool is already started use 'isempty(gcp('nocreate'))'.

Warning: matlabpool will be removed in a future release.

To query the size of an already started parallel pool, query the 'NumWorkers'

property of the pool.

To check if a pool is already started use 'isempty(gcp('nocreate'))'.

Warning: matlabpool will be removed in a future release.

Use parpool instead.

Starting matlabpool using the 'local' profile ...

Error using matlabpool (line 148)

Failed to start a parallel pool. (For information in addition to the causing error,

validate the profile 'local' in the Cluster Profile Manager.)

Error in lme_mass_fit (line 128)

matlabpool(prs);

Error in lme_mass_fit_vw (line 73)

[stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);

Caused by:

Error using parallel.internal.pool.InteractiveClient/start (line 330)

Failed to start pool.

Error using parallel.Job/submit (line 304)

You requested a minimum of 8 workers, but the cluster "local" has the

NumWorkers property set to allow a maximum of 4 workers. To run a

communicating job on more workers than this (up to a maximum of 512 for the

Local cluster), increase the value of the NumWorkers property for the

cluster. The default value of NumWorkers for a Local cluster is the number of

cores on the local machine.
To: freesurfer@nmr.mgh.harvard.edu
From: mreuter@nmr.mgh.harvard.edu
Date: Wed, 14 Oct 2015 10:54:41 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
Hi Pablo,

you should run something like this to get the ni:

[M,Y,ni] = sortData(M,1,Y,sID);  # (sorts the data)
see
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels

hope that helps, Martin

On 10/14/2015 10:43 AM, pablo najt wrote:
Dear FS experts.
I have query about a relating to a previous email (below). I am aiming to run a LME analysis on cross-sectional data from different families and have variable 'family' (number of families) as my NI vector.

My design has three groups and therefore I am not able to use qdec. I am running the matlab commands below and finding some difficulty would really appreciate if you could help out.

Thanks

Pablo

Start analysis as follows:

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');
 %---------------------I input the concatenated .mgh image from preproc and mris_surf2surf-----------------------------------------------------------------------%
3-Fit a vertex-wise lme model with random effects.:
lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);
Here I am getting the following problems:
%-------------------- If I use number of families as my ni get the following------------------------------------------------------------------------------------------------%
lhstats = lme_mass_fit_vw(X, [1 2], lhY, 82, lhcortex);
Error using lme_mass_fit (line 108)
The total number of measurements, indicated by sum(ni), mustbe the same as the number of rows of the design
matrix X
Error in lme_mass_fit_vw (line 73)
[stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);
 My matrix is organised in "family", "group", Sex" and "age" columns".
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');

Date: Thu, 10 Sep 2015 13:44:36 +0000 From: jbernal0019@yahoo.es To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset

Hi Pablo

I think you can use LME to analyze your data by ordering the rows of your design matrix appropriately. You can consider all subjects belonging to the same family as if they were a single subject in a longitudinal analysis. You can put in your design matrix all subjects belonging to family1 first, then all subjects belonging to family 2 and so on. Then the 'ni' required by lme_mass_fit_vw is a vector with the number of subjects in each family as its entries (ordered according to your design matrix). So the length of the 'ni' vector is equal to the number of different families in your data.

Now you can go further and additionally order the rows of your design matrix within each family by age. This will allow you to test the effect of age within family.

When choosing the random effects for your statistical model remember that a random effect can only be the intercept term or any covariate that varies within family. For example you can compare a model with a single random effect for the intercept term against the same model but considering both the intercept term and age as random effects.

Hope that helps

Cheers

-Jorge

De: pablo najt <pablonajt@hotmail.com> Para: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Enviado: Jueves 10 de septiembre de 2015 8:07 Asunto: [Freesurfer] A mixed effect model approach in within subject dataset

Dear Freesurfer users,
I wanted to enquire if anyone had successfully been able to implement Bernal's Linear Mixed Effects (LME) Models in cross-section dataset *not longitudinal* (please see previous thread below). I am willing to perform a LME (3 groups (HC, PT and Unaffected_relatives) and 3 covariates (sex, age, and family) with "family" variable been a within-subject factor. LME will allow to control for the non-independence of data contributed by patients and relatives from the same families.

Thanks in advance!

Pablo

From: michaelnotter@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Wed, 19 Feb 2014 13:10:09 +0100 Subject: [Freesurfer] Analysis of structural data acquired from multiple sites by using a mixed effect model approach

Hi everybody, I want to compare the surface data of 3 groups (GroupA, GroupB and Controlls) but have the problem that they were acquired from 4 different scanner sites. As I can see it, there are three ways how I could tackle this problem: 1. I could use mri_glmfit and create a qdec table / fsgd-file with 12 classes: Class GroupA_site1; Class GroupA_site2,... And then use the contrasts [0.25 0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 -0.25] to compare GroupA to the Controlls. My Problem with this approach is, that the sites don't contribute the same amount of subjects to the analysis. I'm not sure if this could be handled by simply using a weighted contrast. Meaning, if Site1 and Site2 had twice as many subjects than Site3 and Site4, I could modify the contrast to [0.33 0.33 0.17 0.17 0 0 0 0 -0.33 -0.33 -0.17 -0.17]. 2. I could create dummy variables to account for the variability between sites. In this case, I only need to specify 3 classes (Class GroupA; Class GroupB; Class Controlls) in my fsgd-file. And I use a design matrix that has 4 dummy variables at the end, which specify to which site a subject belongs. This approach might work, but I'm not confident that it is the right one. 3. I could use a mixed effect model approach and specify site as a random effect. If I understand it correctly, the mixed effect model approach would be the best one, as it accounts for the variability within sites. Is that correct or are there other issues/better approaches? I tried to implement a mixed effect model by using Bernal's Linear Mixed Effects (LME) Models (http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) but run into some problems. I'm not sure if LME can only be applied on longitudinal data or if my implementation is wrong. I have a design matrix X that specifies the characteristics of each subject per row as follows: Intercept GroupA GroupB Controll Age IQ Site1 Site2 Site3 Site4 1 1 0 0 11.1 99 0 0 1 0 1 0 1 0 11.1 101 0 0 1 0 1 1 0 0 11.4 95 1 0 0 0 1 0 0 1 12.4 100 1 0 0 0 ... As I have no repeated measures, 'ni' is just a vector with length X containing '1's. If I do now the vertex-wise linear mixed-effects estimation, I get the following output: >> stats = lme_mass_fit_vw(X,[7 8 9 10],Y,ni,lhcortex); Starting matlabpool using the 'local' profile ... connected to 8 workers. Starting model fitting at each location ... Location 24994: Index exceeds matrix dimensions. Location 24994: Algorithm did not converge. Initial and final likelihoods: -10000000000, -10000000000. Location 62484: Index exceeds matrix dimensions. Location 62484: Algorithm did not converge. Initial and final likelihoods: -10000000000, -10000000000. ... I've checked the matrix dimensions of X, Y, ni and lhcortex and compared them to the LME mass_univariate example stored in ADNI_Long_50sMCI_vs_50cMCI.mat but couldn't find any divergence. Has anybody encountered similar problems? Is my approach of specifying 'ni' as a vector of'1's even legitimate? Thanks, Michael

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Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
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Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
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Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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