[FieldTrip] Source Reconstruction

[Schoffelen, J.M. (Jan Mathijs)]

Hi Ainsley,

Why would you want to use sensorrealign/electroderealign since you have MEG-data? The former functions may be needed for EEG electrodes, not for MEG sensors.

Best wishes,
Jan-Mathijs


J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow - PI, language in interaction
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands


On 08 Mar 2017, at 07:52, Ainsley Temudo <ainsley.temudo at nyu.edu<mailto:ainsley.temudo at nyu.edu>> wrote:

Hi FieldTrip Experts,

I am trying to perform source reconstruction, and I am having trouble with coregistering my anatomical with the sensors. The MEG system we're using is Yokogawa and the anatomical is a NIFTI file. I get some errors when using  ft_sensorrealign and ft_electroderealign. I will go through the steps I took before getting to this stage, as maybe I have done something wrong.

first I read in my MRI and determine the coordinate system which is LPS.

mriunknown = ft_read_mri('WMCP1011+22+t1mprage.nii');
mri = ft_determine_coordsys(mriunknown, 'interactive','yes')

 next I realign to the CTF coordinate system by marking the NAS LPA, RPA

cfg = [];
cfg.method = 'interactive';
cfg.coordsys = 'ctf';

mri_ctf = ft_volumerealign(cfg, mir);

I read in the sensor information and added in the coordinates for the marker positions. we have five marker positions, the three I picked were the left and right ear markers and the middle forehead marker.

grad=ft_read_sens('srcLocTest01_FT_01.con');





grad.fid.pnt(1,:) = [96.07 3.11 -5.32]./10;
grad.fid.pnt(2,:) = [11.13 75.50 -78.23]./10;
grad.fid.pnt(3,:) = [8.50 -75.09 -64.60]./10;



grad.fid.label = {'NAS' 'LPA' 'RPA'};

I then put the template marker point cordinates  into the configuration which were taken from the mri_ctf

cfg = [];
cfg.method = 'fiducial';
cfg.target.pnt(1,:) = [91.1 3.0 49.2]./10;
cfg.target.pnt(2,:) = [-0.1 70.5 0.0]./10;
cfg.target.pnt(3,:) = [0.1 -70.5 0.0]./10;



cfg.target.label = {'NAS' 'LPA' 'RPA'};



grad_aligned = ft_sensorrealign(cfg, grad);

when I use ft_sensorrealign I get the following errors  :

Undefined function or variable 'lab'.

Error in channelposition (line 314)
n   = size(lab,2);

Error in ft_datatype_sens (line 328)
        [chanpos, chanori, lab] = channelposition(sens);

Error in ft_sensorrealign (line 212)
elec_original = ft_datatype_sens(elec_original); % ensure up-to-date sensor description (Oct 2011)


when I use ft_electroderealign I get the following errors:

Error using ft_fetch_sens (line 192)
no electrodes or gradiometers specified.

Error in ft_electroderealign (line 195)
  elec_original = ft_fetch_sens(cfg);


Hope you can help me figure out why I'm getting these errors.
Thanks,
Ainsley
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J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow - PI, language in interaction
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands



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