[FieldTrip] [Fieldtrip] neuromag source data vertically smeared?

jan-mathijs schoffelen jan.schoffelen at donders.ru.nl
Tue Oct 22 15:13:27 CEST 2013


Hi Hanneke,

I don't know what you expect to see, but to me it is not clear what quantity you are visualizing here (given the units).
Also, note that when you put precomputed spatial filters in the cfg, the lambda specified for the second round of ft_sourceanalysis is not going to change the spatial structure of the result, because the spatial filters are fixed. Also, note that specifying '0.05%' leads to a very tiny regularization. I think that you wanted to specify '5%', which translates to 0.05 times the trace of the csd matrix. Also, even though the cfg.vol will not be used in the second round of ft_sourceanalysis (nor in the first one if you used precomputed leadfields) I don't see the point in fiddling around with the metric units (converting it to 'mm'), but then explicitly stating them to be in 'cm'. Did you not do this when actually computing the leadfields? I hope not.

Best,
Jan-Mathijs



On Oct 22, 2013, at 3:02 PM, <Hanneke.vanDijk at med.uni-duesseldorf.de> <Hanneke.vanDijk at med.uni-duesseldorf.de> wrote:

> Dear all,
>  
> My data (that are recorded with a neuromag306 system) look vertically smeared after sourceanalysis (see attached picture). The sources look like columns. The location (when plotted with method 'surface') looks comparable to the sensor analysis so I am not worried about that. 
>  
> The noise projection (cfg.dics.lambda) is something that I have been playing around with, but other then 'nai amplitude' de- or increases, this does not change the sources 'verticallness'. This indicates to me that this might be the problem... 
>  
> I am wondering if any of you has an idea where I should look to find a solution. 
>  
> Further information:
>  
> I am using a mni-normalised headmodel such as described on the site: http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space but adapted to the neuromag system (I will make changes to the specific site :-) ).
>  
> Then compute the fourier, and do sourceanalysis as follows:
>  
> cfg                     = [];
> cfg.method              = 'dics';
> cfg.grid                = mni_grid;
> cfg.grid.filter         = source.avg.filter; % precomputed filter and leadfield to project all trials through the same filter
> cfg.grid.leadfield   = source.leadfield;
> cfg.vol                 = ft_convert_units(mni_vol,'mm'); % this step is needed somehow...
> cfg.vol.unit           = 'cm';
> cfg.frequency       = 60;
> cfg.latency           = 3;
> cfg.dics.projectnoise   = 'yes';
> cfg.dics.lambda         = '0.05%';
> cfg.dics.normalize      = 'yes';
> cfg.keeptrials          = 'yes';
> cfg.rawtrial            = 'yes';      % project each single trial through the filter
> s = ft_sourceanalysis(cfg, f);
>  
> Thanks in advance for any suggestion!
>  
> Groetjes Hanneke
>  
>  
> __________________________________________
>  
> Hanneke van Dijk, PhD
> http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html
> Institute for Clinical Neuroscience,
> Heinrich Heine Universität Düsseldorf, Germany
> Hanneke.vanDijk at med.uni-duesseldorf.de
> Tel. +49 (0) 211 81 13074  
> __________________________________________                                       
>  
> <source_vertical.jpg>_______________________________________________
> fieldtrip mailing list
> 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
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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