[FieldTrip] ft_sourcestatistics startup memory problem

[Saskia Haegens]

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
>
>
>
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