[FieldTrip] ft_mvaranalysis

Tyler Grummett tyler.grummett at flinders.edu.au
Wed Jun 4 02:41:22 CEST 2014


Hey Jorn,

You were right, it was rank reduced. I tried changing that option that is used if ft_prepare_leadfield ( 'reducerank' = 'no'), but it didnt seem to work.

My code is as follows: (I used an atlas to get the grid coordinates)

            % compute lead field ( apparently source analysis computes
            % lead field anyway
            cfg                 = [];
            cfg.elec            = timelock.elec;
            cfg.vol             = vol;
            cfg.grid.unit       = 'mm';
            cfg.dim = atlas_grid.dim;
            cfg.pos = pos;
            cfg.reducerank = 'no'; % 3 for EEG, 2 for MEG
            cfg.backproject = 'yes';
            cfg.normalize = 'yes'; % if you are not contrasting the activity of interest again another condition or baseline time-window
            grid = ft_prepare_leadfield( cfg);
            
            % Source Analysis: without contrasting condition
            cfg = [];
            cfg.channel = 'EEG';
            cfg.method = 'lcmv';
            cfg.grid = grid;
            cfg.vol = vol;
            cfg.keepfilter = 'yes';
            source = ft_sourceanalysis( cfg, timelock);

Previously I had used the x, y and z grid from the atlas, but I till had a reduced rank.

Any suggestions?

Tyler

*************************

Tyler Grummett ( BBSc, BSc(Hons I))
PhD Candidate
Brain Signals Laboratory
Flinders University
Rm 5A301
Ext 66124

________________________________________
From: fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl> on behalf of "Jörn M. Horschig" <jm.horschig at donders.ru.nl>
Sent: Tuesday, 3 June 2014 6:16 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] ft_mvaranalysis

Hi Tyler,

most likely your data is rank deficient. You can check this by
 >> rank(data.trial{1})

You probably won't get 116 (#channels) as a result. If I remember
correctly your data needs to have full-rank for mvaranalysis.

Best,
Jörn


On 6/3/2014 9:50 AM, Tyler Grummett wrote:
>
> JM,
>
>
> My data has the following format:
>
>
> data =
>
>
> fsample: 500
> sampleinfo: [14x2 double]
> trial: {1x14 cell}
> time: {1x14 cell}
> label: {1x116 cell}
> cfg: [1x1 struct]
>
> I had a look and there are no NaNs or anything. I have tried running
> using the coherence method for connectivity analysis (hence I didnt
> need to use mvaranalysis) and it seemed to work fine.
>
> Can you give me any suggestions as to what the problems with my data
> could be?
>
> Tyler
>
>
>
> *************************
>
> /Tyler Grummett ( BBSc, BSc(Hons I))/
> /PhD Candidate/
> /Brain Signals Laboratory/
> /Flinders University/
> /Rm 5A301/
> /Ext 66124/
> ------------------------------------------------------------------------
> *From:* fieldtrip-bounces at science.ru.nl
> <fieldtrip-bounces at science.ru.nl> on behalf of jan-mathijs schoffelen
> <jan.schoffelen at donders.ru.nl>
> *Sent:* Tuesday, 3 June 2014 5:06 PM
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] ft_mvaranalysis
> This is a low level matlab error and suggests a problem with your data.
>
>
> On Jun 3, 2014, at 9:32 AM, Tyler Grummett
> <tyler.grummett at flinders.edu.au
> <mailto:tyler.grummett at flinders.edu.au>> wrote:
>
>> Using the same code it generates the error:
>>
>> Error using chol
>> Matrix must be positive definite.
>>
>> Error in armorf (line 40)
>> ap(:,:,1) = inv((chol(ap(:,:,1)/Nr*(Nl-1)))');
>>
>> Error in ft_mvaranalysis (line 395)
>> [ar, tmpnoisecov] = armorf(dat, numel(rpt{rlop}),
>> size(tmpdata.trial{1},2),
>> cfg.order);
>>
>>
>>
>> *************************
>>
>> /Tyler Grummett ( BBSc, BSc(Hons I))/
>> /PhD Candidate/
>> /Brain Signals Laboratory/
>> /Flinders University/
>> /Rm 5A301/
>> /Ext 66124/
>> ------------------------------------------------------------------------
>> *From:*fieldtrip-bounces at science.ru.nl
>> <mailto:fieldtrip-bounces at science.ru.nl><fieldtrip-bounces at science.ru.nl
>> <mailto:fieldtrip-bounces at science.ru.nl>> on behalf of jan-mathijs
>> schoffelen <jan.schoffelen at donders.ru.nl
>> <mailto:jan.schoffelen at donders.ru.nl>>
>> *Sent:*Tuesday, 3 June 2014 4:49 PM
>> *To:*FieldTrip discussion list
>> *Subject:*Re: [FieldTrip] ft_mvaranalysis
>> Hi Tyler,
>>
>> Try using ft_hastoolbox(‘bsmart’,1) and then in the cfg for
>> ft_mvaranalysis cfg.toolbox = ‘bsmart’
>>
>> Best,
>> Jan-Mathijs
>>
>> On Jun 3, 2014, at 3:39 AM, Tyler Grummett
>> <tyler.grummett at flinders.edu.au
>> <mailto:tyler.grummett at flinders.edu.au>> wrote:
>>
>>> Hello fieldtrippers,
>>>
>>> Im having problems with ft_mvaranalysis at line 390: [ar, rc, pe] =
>>> mvar(dat', cfg.order, cfg.mvarmethod);
>>>
>>> The error message is:
>>>
>>> Undefined function 'mvar' for input arguments of type 'double'.
>>>
>>> ​ Ive tried looking for the function, but I cant find it. Is it
>>> likely that it is hidden or absent?
>>>
>>> I swear this has worked before on old data, and I didnt update the
>>> toolbox between trying it
>>> with the old data and with the new data. I have now updated the
>>> fieldtrip toolbox and I have
>>> tried running the code again, but no luck.
>>>
>>> Tyler
>>>
>>> *************************
>>>
>>> /Tyler Grummett ( BBSc, BSc(Hons I))/
>>> /PhD Candidate/
>>> /Brain Signals Laboratory/
>>> /Flinders University/
>>> /Rm 5A301/
>>> /Ext 66124/
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> Jan-Mathijs Schoffelen, MD PhD
>>
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>>
>> Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>>
>> J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
>> Telephone: +31-24-3614793
>>
>> http://www.hettaligebrein.nl <http://www.hettaligebrein.nl/>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> Jan-Mathijs Schoffelen, MD PhD
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
> J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
> Telephone: +31-24-3614793
>
> http://www.hettaligebrein.nl
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


--
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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