[FieldTrip] ft_sourcestatistics startup memory problem

[Akiko Ikkai]

Hi Saskia,

Thank you for the quick advise! Removing cfg definitely works well. Each of
the group data is now 1.3G (I also used "single" to convert everything into
single precision), which is definitely manageable. Computation time has
also been reduced to 3 times less now.

Thanks! Akiko

On Sun, Oct 7, 2012 at 2:16 PM, Saskia Haegens <shaegens at gmail.com> wrote:

> Hi Akiko,
>
> In my experience with grandavg source structs, sometimes the cfg
> (that's attached to the data struct) becomes very large and can
> consume a considerable amount of memory. I'm not sure if that's the
> case/problem here, but might be worth checking and removing the cfg.
> You could even use checkconfig to cleanup your cfg with:
> data.cfg = ft_checkconfig(data.cfg, 'checksize', 'yes')
> Hope this helps!
>
> Best,
> Saskia
>
> On Sun, Oct 7, 2012 at 11:36 AM, Akiko Ikkai <akiko.ikkai at gmail.com>
> wrote:
> > Dear Fieldtrip users,
> >
> > I've been trying to run group stats on my EEG source data, which
> contains 14
> > subjects' normalized beamformer data, and having serious swap memory
> issue
> > (not Matlab memory issue, but OS swap memory).
> >
> > I'm trying to contrast 2 conditions (within subject design). Each
> subject's
> > normalized beamformer data (1 condition) is
> >
> > source_lTMI_intNorm =
> >
> >       anatomy: [181x217x181 double]
> >
> >        inside: [181x217x181 logical]
> >
> >           avg: [1x1 struct]
> >
> >     transform: [4x4 double]
> >
> >           dim: [181 217 181]
> >
> >           cfg: [1x1 struct]
> >
> >
> >>whos
> >
> >
> >
> > Name                     Size                Bytes  Class     Attributes
> >
> >   source_lTMI_intNorm      1x1             520114791  struct
> >
> >
> > therefore, when I open all subjects' data ("data1group" and
> "data2group"),
> > it's huge...
> >
> > Name            Size                 Bytes  Class     Attributes
> >
> >   data1group      1x14            5909429438  cell
> >
> >   data2group      1x14            6705652782  cell
> >
> >
> > data1group & data2group are both 1x14 struct (1 cell/subject). Therefore,
> >
> >>data1group{1}
> >
> > anatomy: [181x217x181 double]
> >
> >        inside: [181x217x181 logical]
> >
> >           avg: [1x1 struct]
> >
> >     transform: [4x4 double]
> >
> >           dim: [181 217 181]
> >
> >           cfg: [1x1 struct]
> >
> > So, when I try to run
> >
> > cfg=[];
> >
> >  cfg.dim         = data1group{1}.dim;
> >
> >  cfg.method      = 'montecarlo';
> >
> >  cfg.statistic   = 'depsamplesT';
> >
> >  cfg.parameter   = 'avg.pow';
> >
> >  cfg.correctm    = 'cluster';
> >
> >  cfg.numrandomization = 100;
> >
> >  cfg.alpha       = 0.05;
> >
> >  cfg.tail        = 0;
> >
> >  nsubj=length(data1group);
> >
> >  cfg.design(1,:) = [1:nsubj 1:nsubj];
> >
> >  cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2];
> >
> >  cfg.uvar        = 1;
> >
> >  cfg.ivar        = 2;
> >
> >  stat = ft_sourcestatistics(cfg, data1group{:}, data2group{:});
> >
> >  stat.anatomy = data1group{1}.anatomy;
> >
> >
> > my computer (os 10.6.8, 6G memory) runs out of swap memory (startup
> > memory?), which forces me to quit Matlab. I'm running above processes in
> a
> > function, so I'm not running into Matlab memory error.
> >
> > Could someone help me how it could run more efficiently? I guess
> > cfg.inputfile is not available for ft_sourcestatistics, so I have to
> > eventually load 2 group data in Matlab workspace...?
> >
> > Thank you in advance! Akiko
> >
> > --
> > Akiko Ikkai, Ph.D.
> > Postdoctoral Fellow
> > Department of Psychological and Brain Sciences
> > Johns Hopkins University
> > Ames Hall, 3400 N. Charles St.
> > Baltimore, MD 21218
> >
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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>



-- 
Akiko Ikkai, Ph.D.
Postdoctoral Fellow
Department of Psychological and Brain Sciences
Johns Hopkins University
Ames Hall, 3400 N. Charles St.
Baltimore, MD 21218
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