[FieldTrip] problem aligning MRI with gradiometer

[Luisa Frei]

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
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