The LME toolbox will create a text file ('parfor_progress1.txt') in
Matlab's present working directory to indicate its progress in
processing each vertex.

To create this file it needs to have write permissions in Matlab's
present working directory.

I speculate that your present working directory in Matlab is the root
directory '/' where the toolbox cannot create a file.

The solution would be to not run the scripts from '/', but to set the
Matlab working directory to another directory where you have write
permissions.

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: Tue, 6 Mar 2018 15:17:31 +0100

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.Diers@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@dzn
> > e.
> > 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@d
> > > zn
> > > 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 <freesur...@nmr.mgh.harvard.ed
> > > u>
> > > 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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