Problem while using prepare_leadfield with parameterscfg.resolution and cfg.inwardshift

Ingmar Schneider Ingmar.Schneider at BIO.UNI-GIESSEN.DE
Tue Apr 22 09:52:09 CEST 2008


Hello again,

what you say is completely right and my problem is related to the
problem described in the FAQ. As I tried to explain in the last mail and
as you say: A reduction of the inwardshift (i.e. to a negative value)
results in a leadfield, that covers the whole anatomy data. But if I
simultaneously try to improve the resolution (i.e. to 0.5cm) the
resulting field is smaller than the one with the default
resolution-value of 1cm. I played with some combinations, but i never
really got a suiting leadfield.
I am using data from a VSM MedTech CTF-MEG with 275 channels and here's
an excerpt of the Matlab-code to further specify my analysis. These
specifications actually deliver a leadfield, that covers most of the
anatomy, but in a poor resolution.

 %Preparation of the head model
    [vol, hdmcfg]=prepare_singleshell([], segmentedmriF); % Single sphere
    save(MRIoutname, 'vol', 'hdmcfg', '-append', '-v7.3');
    clear segmentedmriF;

    %Preparation of the Leadfield for a specific dataset
    filename        = strcat(SubjectID,'_10Hz_Redef_CSDM_20HzBin.mat');
    fullname        = strcat(INpath, filename);
    load(fullname);         % Load redefined data file with gradiometers
etc. for leadfield generation

    cfg         = [];
    cfg.grad    = freqPost.grad;
    cfg.vol     = vol;
    cfg.inwardshift = -1.5;
    cfg.resolution = 1;
    cfg.reducerank = 2;
    cfg.channel    = {'MEG', '-MLP12', '-MRC14', '-MLT41', '-MRC25',
'-MRP56', '-MRT21', '-MLO21', '-MRO44', '-MRT47'};
    cfg.xgrid = 'auto';
    cfg.ygrid = 'auto';
    cfg.zgrid = 'auto';
    [LFgrid]    = prepare_leadfield(cfg);

I hope this helps a bit to clarify my problem and the information is
useful to you.

Best regards,
Ingmar



Robert Oostenveld schrieb:
> Hi Ingmar
>
> Although your question/problem is not completely clear to me, I
> suspect it to be related to
>
> http://www2.ru.nl/fcdonders/fieldtrip/doku.php?id=fieldtrip:documentation:frequently_asked_questions#why_is_there_a_rim_around_the_brain_for_which_the_source_reconstruction_is_not_computed
>
>
> In general fieldtrip tries to make a dipole grid that is just inside
> the brain but as close as possible to the brain surface. Some volume
> conduction models are not fitted to the brain surface however, but to
> the skin surface. In those cases the cfg.inwardshift option tries to
> get an estimate of the brain surface from the skin surface, in order
> to achieve teh same tight fit of the dipole grid in the brain and to
> prevent the solution to be computed for dipoles in teh skull or skin.
>
> However, with a low resolution and a grid that fits exactly in the
> brain you tend to get the problem as outlined in the FAQ. Therfore it
> can be usefull to play with the cfg.inwardshift parameter. You can set
> it to a negative number, i.e. inwardshift=-2.5, which results in a
> 2.5cm _outwardshift_ of the source compartment boundary.
>
> I hope this helps, if not then please ask again with more
> specifications of your analysis (what kind of MEG, what kind of volume
> model, etc).
>
> best regards,
> Robert
>
>
> On 13 Feb 2008, at 15:36, Ingmar Schneider wrote:
>> Hello everybody,
>>
>> I am currently trying to analyze my MEG data with the DICS beamforming
>> technique. While preparing my leadfield grid via the prepare_leadfield.m
>> function I stumbled across a problem I don't understand. Every time I
>> try to
>> decrease the inwardshift to suit the leadfield upon my anatomy data
>> and at
>> the same time increase the resolution the resulting grid is even
>> smaller,
>> than without specification.
>>
>> For example applying the following parameters reduces the size of the
>> resulting grid instead of increasing its volume:
>> cfg.inwardshift = -1.5; %Increasing the grid size to cover the anatomy
>> cfg.resoltion = 0.5;    %[cm]
>>
>> Without the cfg.resolution parameter a reduction of cfg.inwardshift
>> results
>> in the desired bigger leadfield grid which eventually fits upon the MRI
>> data. Are these factors intertwined in the calculations so that one
>> effects
>> the other in the course of calculation?
>>
>> I hope someone can help me solve this little problem and am grateful
>> for any
>> kind of hint.
>>
>> Regards,
>> Ingmar
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.



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