[FieldTrip] ft_mvaranalysis
"Jörn M. Horschig"
jm.horschig at donders.ru.nl
Wed Jun 4 09:42:27 CEST 2014
Hi Tyler,
I thought you are talking about mvaranalysis - why is the code you've
pasted about leadfields and lcmv beamforming?
Best,
Jörn
On 6/4/2014 3:15 AM, Tyler Grummett wrote:
> Jorn,
>
> There is an additional issue of interpolating the data and then plotting it with ft_sourceplot.
>
> I have hit a wall of issues haha
>
> 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 Tyler Grummett <tyler.grummett at flinders.edu.au>
> Sent: Wednesday, 4 June 2014 10:11 AM
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] ft_mvaranalysis
>
> 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
>
> _______________________________________________
> 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
--
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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