[FieldTrip] Regarding headmodel construction

Susmita Sen susmitasen.ece at gmail.com
Fri Sep 30 19:16:52 CEST 2016

I am Susmita Sen, MS research scholar in the dept of Electronics and
Electrical Communication Engineering, IIT Kharagpur.
      I am currently working on MEG data recorded by yokogawa system. I
want to perform source reconstruction on the data. However, I do not have
the MRI data along with that. so, I have planned to use the standard MRI
provided by fieldtrip (downloaded from https://github.com/fieldtrip/

For preparing the head model I have followed the steps provided in the
fieldtrip tutorial (http://www.fieldtriptoolbox.org/tutorial/headmodel_meg

%% align the coordinate system
load('standard_mri.mat'); % load mri data

cfg = [];
cfg.method = 'interactive';
cfg.coordsys = 'yokogawa';
cfg.snapshot     = 'yes';
[mri_aligned] = ft_volumerealign(cfg,mri);

cfg           = [];
cfg.output    = 'brain';
segmentedmri  = ft_volumesegment(cfg, mri_aligned);

%% create headmodel
cfg = [];
vol = ft_prepare_headmodel(cfg, segmentedmri);

%% visualize
load grad % load gradiometer info
vol = ft_convert_units(vol,'cm');  % the gradiometer info is given in cm

ft_plot_sens(grad, 'style', '*b');
hold on

while aligning the coordinate system I have chosen fiducial points (naison,
LPA and RPA) using the instruction given by http://neuroimage.usc.edu/

I am attaching the figures that display the shape of the 'vol' along with
the position of the sensors (from different viewing angle). However, I
doubt the headmodel is corrected prepared (It dosen't look alike the figure
given in the tutorial). It seems I have made some mistakes, but I am not
able to detect it. I would be very thankful if you can help me in this

Thanks and Regards,
Susmita Sen
Research Scholar
Audio and Bio Signal Processing Lab.
E & ECE Dept.
IIT Kharagpur
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