[FieldTrip] ft_sourcestatistics startup memory problem
Akiko Ikkai
akiko.ikkai at gmail.com
Mon Oct 22 19:37:59 CEST 2012
Hi Johanna,
you are right! specifying cfg.grid = grid; was the key; ft_sourceanalysis
for each condition runs to the completion :)
However, since my data is EEG and the electrode locations vary (hence the
grid coordinates vary) between subjects, running stats across subjects
without normalizing might be causing a problem. For example, the first 3
points in subject1's .pos are (after creating template grid etc.., and run
ft_sourceanalysis using MNI grid):
d1group{1}.pos(1:3,:)
ans =
-8.7000 -7.5000 -7.6000
-7.7000 -7.5000 -7.6000
-6.7000 -7.5000 -7.6000
and the same points for the subject2's are:
d1group{2}.pos(1:3,:)
ans =
-8.3000 -7.6000 -8.2000
-7.3000 -7.6000 -8.2000
-6.3000 -7.6000 -8.2000
So when I try to run ft_sourcestatistics. I get an error message:
??? Error using ==> statistics_wrapper at 109
grid locations of the source reconstructions do not match, use
NORMALISEVOLUME
first
Error in ==> ft_sourcestatistics at 100
[stat, cfg] = statistics_wrapper(cfg, varargin{:});
Perhaps I should interpolate and normalize each subject, and run group
stats afterall?
Thanks! Akiko
On Sun, Oct 21, 2012 at 11:32 AM, Johanna Zumer <johanna.zumer at donders.ru.nl
> wrote:
> Hi Akiko,
>
> Can you type 'dbstop if error' before running the last step, so that
> it goes to debug mode when it crashes there? What are the sizes of
> 'filt' and 'Cf' for the 40th position?
>
> Another thing to try is, during your last call to ft_sourceanalysis,
> cfg = [];
> cfg.grid = grid;
> cfg.grid.filter = source_common.avg.filter;
>
> so that all the .inside and .outside information is transfered as well.
>
> A note to all users: you can skip the first step by loading the
> precomuted template grids in */fieldtrip/template/sourcemodel.
>
> Cheers,
> Johanna
>
>
> 2012/10/20 Akiko Ikkai <akiko.ikkai at gmail.com>:
> > Hi,
> >
> > So I have followed Johanna and Stephan's advise to create template_grid
> and
> > each subject's grid from MNI image, which is now 1cm spacing instead of
> > .5cm. These steps seem to run, and I'm able to create a common spatial
> > filter to run beamformer using DICS. However, I get an error when I apply
> > the commom filter to each condition.
> >
> > I had to tweak a few things on example on the page
> >
> http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s[]=template&s[]=grid
> > , since my data is EEG and electrode locations vary between subjects,
> such
> > that:
> >
> > cfg = [];
> > cfg.grid.xgrid = -20:1:20;
> > cfg.grid.ygrid = -20:1:20;
> > cfg.grid.zgrid = -20:1:20;
> > cfg.grid.tight = 'yes';
> > cfg.inwardshift = -1.5;
> > cfg.vol = template_vol;
> > cfg.elec = ft_data.elec; % individual sub's electrode locations: had to
> add
> > this (got error otherwise)
> > template_grid = ft_prepare_sourcemodel(cfg);
> >
> > then
> > cfg = [];
> > cfg.grid.warpmni = 'yes';
> > cfg.grid.template = template_grid;
> > cfg.grid.nonlinear = 'yes';
> > cfg.mri = mri_aligned;
> > cfg.elec = ft_data.elec; % individual sub's electrode locations: had to
> add
> > this (got error otherwise)
> > grid = ft_prepare_sourcemodel(cfg);
> >
> > These create grids in MNI space, both for template and individual fine.
> To
> > create a common spatial filter, I run the following command, which runs:
> > cfg = [];
> > cfg.grid.pos = grid.pos;
> > cfg.grid.dim = grid.dim;
> > cfg.grid.inside = grid.inside;
> > cfg.grid.outside = grid.outside;
> > cfg.inwardshift = -1.5;
> > cfg.vol = vol_cm;
> > cfg.channel = {'all'};
> > cfg.frequency = 10.5;
> > cfg.method = 'dics';
> > cfg.dics.projectnoise = 'yes';
> > cfg.dics.keepfilter = 'yes';
> > cfg.dics.feedback = 'no';
> > source_common = ft_sourceanalysis(cfg, freq_common);
> >
> > however, when I apply this spatial filter to a task condition, I get an
> > error message
> > cfg = [];
> > cfg.elec = freq_common.elec;
> > cfg.grid.pos = source_common.pos;
> > cfg.grid.filter = source_common.avg.filter;
> > cfg.inwardshift = -1.5;
> > cfg.vol = vol_cm;
> > cfg.channel = {'all'};
> > cfg.frequency = 10.5;
> > cfg.method = 'dics';
> > cfg.dics.projectnoise = 'yes';
> > cfg.dics.keepfilter = 'yes';
> > cfg.dics.feedback = 'no';
> > source_itemL = ft_sourceanalysis(cfg, freq_itemL);
> > source_itemL.unit = 'cm';
> >
> > ??? Error using ==> mtimes
> > Inner matrix dimensions must agree.
> >
> > Error in ==> beamformer_dics at 316
> > csd = filt * Cf * ctranspose(filt); % Gross
> > eqn. 4
> > and 5
> >
> > Error in ==> ft_sourceanalysis at 588
> > dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)),
> > optarg{:});
> >
> > The error occurs when dip.pos = 40 (i.e. it runs fine 1-39). I can't spot
> > where exactly the error is originating from. Am I missing some steps
> when I
> > create template grids that I feed into ft_sourceanalysis?
> >
> > Thank you in advance for your help! Akiko
> >
> >
> > On Thu, Oct 18, 2012 at 4:29 PM, Akiko Ikkai <akiko.ikkai at gmail.com>
> wrote:
> >>
> >> Hi Everyone,
> >>
> >> Thank you very much for your advise. I just came back from SfN, and just
> >> found your replies, so I will test these options and report back what I
> >> find.
> >>
> >> Thank you again! Akiko
> >>
> >>
> >> On Mon, Oct 8, 2012 at 6:14 AM, Stephen Whitmarsh
> >> <stephen.whitmarsh at gmail.com> wrote:
> >>>
> >>> Hi Akiko!
> >>>
> >>> Just to chime in - your source grid is very, very large indeed!
> ALthough
> >>> I started with a very fine grid, at one point I also had to downside it
> >>> (going to 5mm), and had to stop using interpolated source data for
> stats and
> >>> the like. Johanna's suggestion will certainly do the trick and it will
> speed
> >>> up your analysis enormously as well. You then only need to do
> interpolate
> >>> for plotting purposes.
> >>>
> >>> all the best,
> >>> Stephen
> >>>
> >>>
> >>> On 8 October 2012 12:02, Johanna Zumer <johanna.zumer at donders.ru.nl>
> >>> wrote:
> >>>>
> >>>> Hi Akiko,
> >>>>
> >>>> In addition to Saskia's comment (which is very useful!) remember also
> >>>> that if you create the subject's grid from the warped MNI template
> grid
> >>>> (explained here
> >>>>
> http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s[]=template&s[]=grid
> )
> >>>> then you can keep each subject's source data in a 'source' structure
> with
> >>>> .pos field and still do group level statistics, without need to
> convert to
> >>>> 'volume' structure which upsamples the spatial resolution perhaps
> >>>> artificially too high.
> >>>>
> >>>> Cheers,
> >>>> Johanna
> >>>>
> >>>>
> >>>> 2012/10/7 Akiko Ikkai <akiko.ikkai at gmail.com>
> >>>>>
> >>>>> 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
> >>>>>> _______________________________________________
> >>>>>> fieldtrip mailing list
> >>>>>> fieldtrip at donders.ru.nl
> >>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> 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
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> fieldtrip mailing list
> >>>> fieldtrip at donders.ru.nl
> >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> fieldtrip mailing list
> >>> fieldtrip at donders.ru.nl
> >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >>
> >>
> >>
> >>
> >> --
> >> Akiko Ikkai, Ph.D.
> >> Postdoctoral Fellow
> >> Department of Psychological and Brain Sciences
> >> Johns Hopkins University
> >> Ames Hall, 3400 N. Charles St.
> >> Baltimore, MD 21218
> >>
> >>
> >
> >
> >
> > --
> > 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
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
--
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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