After downloading version 6.0. and running lhstats = lme_mass_fit_vw(X,[1 
2],Y,ni,lhcortex,[],1), I received the following errors.

Error using parfor_progress (line 17)
Do you have write permissions for /?

Error in lme_mass_fit (line 155)
fn = parfor_progress('init',nv);

Error in lme_mass_fit_vw (line 73)
[stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);

Thoughts?

Mayank
> On Mar 6, 2018, at 7:08 AM, Diers, Kersten /DZNE <kersten.di...@dzne.de> 
> wrote:
> 
> ATTENTION: This email originated from a sender outside of MCW. Use caution 
> when clicking on links or opening attachments.
> ________________________________
> 
> Yes,
> 
> my understanding is the same.
> 
> The LME toolbox can in a way be regarded as a post-processing add-on to
> Freesurfer. The only interface with Freesurfer are the read/write
> functions, everything else is to the best of my knowledge independent
> of Freesurfer. So I cannot see any problems in using the newer version
> of the LME toolbox with data from Freesurfer 5.3.
> 
> Needless to say, this does not affect the usual recommendation, which
> is that Freesurfer versions should not be mixed in general.
> 
> Best,
> 
> Kersten
> 
> 
> 
> ------Original Message-----
> From: "Kaushal, Mayank" <mkaus...@mcw.edu>
> Reply-to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Running Linear Mixed Effects (LME) Model
> Date: Mon, 5 Mar 2018 20:47:36 +0100
> 
> The version string I have been using:
> $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
> So, it appears that I do indeed have the older version.
> 
> I am running Matlab 2017a, which is a relatively newer version.
> 
> Before I proceed with using LME toolbox from a freesurfer 6.0, I would
> appreciate your input on the following.
> 
> My understanding is that LME toolbox is used for statistical analysis
> and is independent of the freesurfer version performing the actual
> cortical thickness analysis. So, in theory, if I import cortical
> thickness data processed in version 5.3, I should still be able to run
> the LME toolbox from a version 6.0.
> So, can I input the files processed by freesurfer 5.3 (files that have
> been processed till mris_preproc and mri_surf2surf) and simply use the
> LME toolbox from a version 6.0 to perform the statistical analysis?
> 
> Mayank
>> 
>> On Mar 5, 2018, at 1:29 PM, Diers, Kersten /DZNE <Kersten.Diers@dzne.
>> de> wrote:
>> 
>> ATTENTION: This email originated from a sender outside of MCW. Use
>> caution when clicking on links or opening attachments.
>> ________________________________
>> 
>> Hi,
>> 
>> thanks for the additional information.
>> 
>> I believe that we are dealing with a version issue now.
>> 
>> Specifically, I have so far been testing with an LME toolbox from a
>> Freesurfer 6.0 version on Matlab R2016a. In that sense, there is no
>> need for a separate download of the LME scripts, since they are
>> already
>> included within the freesurfer directory (e.g.
>> 'freesurfer/matlab/lme').
>> 
>> It is primarily the 'lme_mass_fit.m' script, which throws the current
>> error. Could you please check your version of this script (type 'help
>> lme_mass_fit.m')?
>> 
>> Within my 5.3 installation, the version string is:
>> % $Revision: 1.1.2.2 $  $Date: 2013/02/23 21:08:10 $
>> 
>> Within my 6.0 installation, the version string is:
>> $Revision: 1.3 $  $Date: 2016/04/08 19:39:24 $
>> 
>> Unfortunately, the version string of the 'lme_mass_fit.m' script
>> within
>> a toolbox that I just downloaded from the LME website is the most
>> ancient one:
>> % $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
>> 
>> When I use the 1.1.1.1 version instead of the one that is included
>> within Freesurfer 6.0, I can replicate the problem reported in your
>> current mail. With the 1.3 version I have no issues.
>> 
>> As far as I know, the 'lme_mass_fit.m' script was updated to
>> accommodate the changes in Matlab's way of doing the parallel
>> processing. In older Matlab versions this was done using the
>> 'matlabpool' command, but this was replaced by 'parpool', which is -
>> to
>> my knowledge - the only way of running parallel processing with
>> recent
>> Matlab versions. The LME toolbox was originally only tailored to the
>> 'matlabpool' command, but has later been adapted to also include the
>> 'parpool' command.
>> 
>> Assuming that you are using a relatively recent Matlab version, the
>> use
>> of earlier vs. later versions of the toolbox would explain our
>> respective observations.
>> 
>> All in all, I currently see no way of getting an older version of the
>> LME toolbox to run with a current Matlab version - except from
>> modifying the code itself. So my suggestion would be to just use the
>> newer LME toolbox that is shipped with Freesurfer 6.0.
>> 
>> Let us know if I am mistaken or if there are further issues.
>> 
>> Best regards,
>> 
>> Kersten
>> 
>> 
>> -----Original Message-----
>> From: "Kaushal, Mayank" <mkaus...@mcw.edu>
>> Reply-to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Running Linear Mixed Effects (LME) Model
>> Date: Mon, 5 Mar 2018 16:34:14 +0100
>> 
>> Thanks for the quick response Kersten.
>> 
>> I tried all the potential suggestions mentioned in your post but
>> still
>> no luck.
>> 
>> 
>> Here’s the summary:
>> 
>> 
>> lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],1)
>> Undefined function or variable 'matlabpool'.
>> 
>> Error in lme_mass_fit (line 124)
>>   if (matlabpool('size') > 0)
>> 
>> Error in lme_mass_fit_vw (line 73)
>> [stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);
>> 
>> 
>> lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],2)
>> Undefined function or variable 'matlabpool'.
>> 
>> Error in lme_mass_fit (line 123)
>> if (prs==1) || (matlabpool('size') ~= prs)
>> 
>> Error in lme_mass_fit_vw (line 73)
>> [stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);
>> 
>> 
>> The "automatically create a parallel pool" was already deselected in
>> my
>> case.
>> 
>> Also, I am using freesurfer 5.3 with LME toolbox downloaded from the
>> freesurfer website.
>> 
>> Mayank
>>> 
>>> 
>>> On Mar 5, 2018, at 9:12 AM, Diers, Kersten /DZNE <Kersten.Diers@dzn
>>> e.
>>> de> wrote:
>>> 
>>> ATTENTION: This email originated from a sender outside of MCW. Use
>>> caution when clicking on links or opening attachments.
>>> ________________________________
>>> 
>>> Hi,
>>> 
>>> you might try supplying an additional command-line argument while
>>> calling the 'lme_mass_fit_vw' function:
>>> 
>>> lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],1)
>>> 
>>> This will tell Matlab to use only one worker. Further documentation
>>> on
>>> this additional argument can be obtained by typing 'help
>>> lme_mass_fit_vw' at the Matlab prompt.
>>> 
>>> To get this working with my Matlab installation, I additionally had
>>> to deselect the "Automatically create parallel pool (if one doesn't
>>> already exist) when parallel keywords (e.g., parfor) are executed."
>>> option. This can be found in Matlab's preferences menu (--> see the
>>> Parallel Computing toolbox section).
>>> 
>>> As an alternative, using two workers might also be an option in
>>> your
>>> case:
>>> 
>>> lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],2)
>>> 
>>> To get this alternative approach working, I did not have to change
>>> the
>>> Matlab preferences.
>>> 
>>> Hope this helps,
>>> 
>>> Kersten
>>> 
>>> 
>>> -----Original Message-----
>>> From: "Kaushal, Mayank" <mkaus...@mcw.edu>
>>> Reply-to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>> To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
>>> Subject: [Freesurfer] Running Linear Mixed Effects (LME) Model
>>> Date: Sun, 4 Mar 2018 23:56:03 +0100
>>> 
>>> Dear Freesurfer Community,
>>> 
>>> Running lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex); gives the
>>> following error,
>>> Starting parallel pool (parpool) using the 'local' profile ...
>>> Error using parpool (line 104)
>>> You requested a minimum of 8 workers, but the cluster "local" has
>>> the
>>> NumWorkers property set to allow a maximum of 2 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.
>>> 
>>> Error in lme_mass_fit (line 137)
>>>              parpool(prs);
>>> 
>>> Error in lme_mass_fit_vw (line 73)
>>> [stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);
>>> 
>>> I am running Matlab on a personal MacBook Pro, 2.4 GHz Intel Core
>>> i5,
>>> 8
>>> GB 1600 MHz DDR3.
>>> 
>>> I have researched the forum on how to stop the function from trying
>>> to
>>> initiate parallel processing but so far haven’t been able figure
>>> out
>>> how to overcome this.
>>> 
>>> Any help would be much appreciated.
>>> 
>>> 
>>> Mayank Kaushal MD MBA
>>> Postdoctoral Fellow
>>> Department of Neurosurgery
>>> Medical College of Wisconsin
>>> 
>>> 
>>> 
>>> _______________________________________________
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