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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