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

[Sameer Walawalkar]

Dear Eric,

Thank you for you reply.

I am now trying to use clusterrandanalysis. It looks for data.dof. So for
freqanalysis I have

cfgCSD.method = 'mtmfft';
cfgCSD.keeptrials = 'yes' ;
cfgCSD.keeptapers = 'yes' ;
cfgCSD.calcdof    = 'yes';

this leads to error on line 540

if calcdof
   freq.dof=2*repmat(cumtapcnt,[1,numfoi]);
end;

Basically, numfoi is not defined before this statement, and only appears
once throughout the file. Should it be numel(foi) ?

Best,
Sameer

p.s: incidently,
  ~exist(cumtapcnt) gives error. MATLAB needs ~exist('cumtapcnt')
 	(it could be a version problem).





On Mon, 2 Jul 2007, Eric Maris wrote:

> 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.
>
>

----------------------------------
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.