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

[Hanneke van Dijk]

Hi Jan-Mathijs,

schaam schaam,

The unit thing must have been fixed! So problem fixed, thanks so much!

Groetjes uit Duesseldorf!

Hanneke

Groetjes Hanneke


On Tue, Oct 22, 2013 at 4:53 PM, Hanneke van Dijk <
hanneke.p.van.dijk at gmail.com> wrote:

> 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
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
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>>
>
>
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