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

[Hanneke van Dijk]

Hi Jan-Mathijs,

Thanks for your quick reply. I will go through your comments one by one:

1. The plot shows the nai, and in stead of these straight vertical lines
going even into the center of the brain, I expected to see blobs.
2. In the precomputed filters I have used the same lambda, I should remove
the cfg from this part. I have used cfg.dics.lambda from 0.05 to 50 and as
I said this only changes the 'power' but not the structure of the data.
3. About the cfg.vol. I have been fidling around with the units for quite
some time, but this is the only way the functional data will not end up the
size of a pea in the anatomical data. I think this has to do with
ctf/neuromag/spm coordinate system differences that are not yet fixed in
FieldTrip?

But it seems that there is no obvious thing that could be happening then?

Groetjes Hanneke






On Tue, Oct 22, 2013 at 3:13 PM, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:

> 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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