using cfg.correctm = 'cluster' and related memory issues.

[Eric Maris]

Dear Sameer,


I forgot to mention that the analyses on which is reported in the J.
Neuroscience Methods paper were done using Clusterrandanalysis.m, which is
an older version of the Fieldtrip statistics. For testing coherence
differences, Clusterrandanalysis.m is better suited than the new statistics
functions.


Good luck,

Eric

dr. Eric Maris
NICI/Biological Psychology and
F.C. Donders Center for Cognitive NeuroImaging
University of Nijmegen
P.O. Box 9104
6500 HE Nijmegen
The Netherlands
T:+31 24 3612651 (NICI)
T:+31 24 3610754 (FCDC)
F:+31 24 3616066 (NICI)
E: maris at nici.ru.nl
MSc Cognitive Neuroscience :www.ru.nl/master/cns/


> -----Original Message-----
> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
Behalf Of
> Sameer Walawalkar
> Sent: Monday, July 02, 2007 7:05 PM
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: [FIELDTRIP] using cfg.correctm = 'cluster' and related memory
issues.
>
> Hello,
>
> I am running into memory issues while trying to do non-parametric
> statistical testing for coherence differences for my Neuromag 306 data.
>
>   The statement causing overflow is line 277 in statistics_montecarlo:
> statrand = zeros(size(statobs,1), size(res,1));
> This would be a matrix of size 50631525 X 100 corresponding to some 40 GB!
> (Am I correct in assuming that the 100 is from cfg.numrandomization)?
>
> This statement is evoked if cfg.correctm = 'cluster';
> I could use cfg.correctm = max but I dont think this will do the right
> analysis.
>
> The one thing I can think of is changing cfg.channelcmb to try and reduce
> the number of combinations tried (but is not very preferable atleast right
> now). Is there anything else that comes to mind?
>
> The cfg I am using and other info is added below.
>
> Thank you for your time and help.
> sameer
>
> >>cfg = [];
> cfg.channelcmb = {'MEG' 'MEG'};
> cfg.method = 'montecarlo';
> cfg.statistic = 'indepsamplesZcoh';
> cfg.clusteralpha = 0.05;
> cfg.clusterstatistic = 'maxsum';
> cfg.clusterthreshold = 'nonparametric';
> cfg.minnbchan = 2;
> cfg.tail = 0;
> cfg.clustertail = 0;
> cfg.alpha = 0.05;
> cfg.numrandomization = 100; % make it larger for better testing
> cfg.precision          = 'single'; % experimenting to save memory
> cfg.label = CSD_LL_200_400.label ;
> cfg.channelcmb = CSD_LL_200_400.labelcmb;
>
>
> [statistics] = freqstatistics(cfg, CSD_LL_200_400 , CSD_RR_200_400);
>
> Note: I use Cross Spectral density instead of coherence as coherence does
> not keep trials.
>
> At the debug prompt after the error I have:
>
> K>> whos
>    Name                  Size                   Bytes  Class
> Attributes
>
>    Nrand                 1x1                        8  double
>    cfg                   1x1                 60159588  struct
>    dat              326655x127              331881480  single
> complex
>    design                1x127                   1016  double
>    res                 100x1x127               101600  double
>    statfull              1x1                405052324  struct
>    statfun               1x1                       16  function_handle
>    statobs        50631525x1                405052200  double
>    time_eval             1x1                        8  double
>    time_pre              1x1                        8  double
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip
> toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.