[FieldTrip] problem aligning MRI with gradiometer

[Allison Connolly]

Thanks that seemed to help the scaling issue. However, my beamforming is
still not producing results. There is a huge bias towards the center of the
head, even though I accounted for the neural activity index. It seems like
the beamforming is just projecting everything inwards. I'm not sure where to
go from here. Do you have any suggestions on different configuration
settings I could try for the beamforming?

-Allison

On Fri, Feb 11, 2011 at 4:02 PM, Luisa Frei <l.frei at psy.gla.ac.uk> wrote:

> Hi Alison,
> how do you change the units? I convert them using:
>
> data.grad=ft_convert_units(data.grad,'cm')
>
> Maybe this helps.
>
> Luisa
>
>
> On 11 Feb 2011, at 21:19, Allison Connolly wrote:
>
>  Hello,
>>
>> I am trying to perform beamforming on some MEG data (148 channels). I have
>> the dicom files for the MRI, and I have converted them to .img and .hdr
>> files using Curry.
>> I am importing them into fieldtrip via
>> mri=ft_read_mri('MRI.img').
>>
>> Then I manually declaring the fiducials with
>> cfg.method                  = 'interactive';
>> mrialign                    = ft_volumerealign(cfg, mri);
>>
>> Then segmenting with
>> cfg = [];
>> cfg.write        = 'no';
>> [segment] = ft_volumesegment(cfg, mri);
>>
>> Then creating the head model with
>> cfg = [];
>> cfg.smooth                  = 'no';
>> vol = ft_prepare_singleshell(cfg, segment);
>>
>> Then creating the grid with
>> cfg                 = [];
>> cfg.grad            = freq.grad;
>> cfg.vol             = vol;
>> cfg.reducerank      = 'no';
>> cfg.channel                 = {'MEG','-TRIGGER','-RESPONSE',...
>>     '-UACurrent','-MxA','-MyA','-MzA','-GxxA','-GyxA','-GyyA',...
>>     '-GzyA','-GzxA','-MxaA','-MyaA','-MzaA','-E1','-E2','-E3','-E4'};
>> cfg.grid.xgrid              = [-10:0.5:15]; % adjust according to vol
>> cfg.grid.ygrid              = [-15:0.5:15]; % adjust according to vol
>> cfg.grid.zgrid              = [-10:0.5:15]; % adjust according to vol
>> [grid] = ft_prepare_leadfield(cfg);
>>
>> I am importing my MEG data with
>> cfg = [];  % empty configuration
>> cfg.dataset                 = 'C:/MEG
>> Study/Subjectd001/d001/Billy_180s/06 at -09@-10 at _19_41/4/c,rfhp0.1Hz';
>> cfg.trialfun                = 'trialfun_general';
>> cfg.trialdef.triallength    = 2;  % duration in seconds
>> cfg.trialdef.ntrials        = inf;  % number of trials, inf results in as
>> many as possible
>> cfg                         = ft_definetrial(cfg);
>>
>> % preprocess the data
>> cfg.channel                 = {'MEG','-TRIGGER','-RESPONSE',...
>>    '-UACurrent','-MxA','-MyA','-MzA','-GxxA','-GyxA','-GyyA',...
>>    '-GzyA','-GzxA','-MxaA','-MyaA','-MzaA','-E1','-E2','-E3','-E4'}; %read
>> all MEG channels except those with '-'
>> cfg.lpfilter                = 'yes';
>> cfg.lpfreq                  = 200;
>> cfg.bsfilter                = 'yes'; %60 Hz noise
>> cfg.bsfreq                  = [58 62];
>>
>> data = ft_preprocessing(cfg);
>>
>> In the end, when I go to plot them all on the same graph, the head model
>> seems to be 100 times larger than the gradiometer sensors (they appear as a
>> small ball in the middle of the head). I've tried adjusting the grad.unit
>> parameter from 'm' to 'cm', but it doesn't help the downstream frequency,
>> leadfield, and source analysis.
>>
>> Can someone tell me how to ensure the gradiometer and mri/grid are on the
>> same scale so I can be sure I have the right model for my beamforming?
>>
>> Thank you,
>> -Allison
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
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