[FieldTrip] Regarding headmodel construction

Simon Homolle s.homolle at donders.ru.nl
Mon Oct 3 10:19:48 CEST 2016

Dear Susmita,

I used your code and could reproduce the same results. The step that goes wrong here is the segmentation step.

cfg           = [];
cfg.output    = {'brain','skull','scalp'};
segmentedmri  = ft_volumesegment(cfg, mri_aligned);
seg_i = ft_datatype_segmentation(segmentedmri,'segmentationstyle','indexed');
cfg              = [];
cfg.funparameter = 'seg';
cfg.funcolormap  = lines(6); % distinct color per tissue
cfg.location     = 'center';
cfg.atlas        = seg_i;    % the segmentation can also be used as atlas 
ft_sourceplot(cfg, seg_i);

I segmented additionally to the scalp the brain and the skull tissues as well so that you can clearly see whats going on. 

You should tweak the cfg for the ft_volumesegment to improve your pipeline.

Best regards,

Simon Homölle
PhD Candidate
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Phone: +31-(0)24-36-65059

> On 30 Sep 2016, at 19:16, Susmita Sen <susmitasen.ece at gmail.com> wrote:
> 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/fieldtrip/blob/master/template/headmodel/standard_mri.mat <https://github.com/fieldtrip/fieldtrip/blob/master/template/headmodel/standard_mri.mat>).
> For preparing the head model I have followed the steps provided in the fieldtrip tutorial (http://www.fieldtriptoolbox.org/tutorial/headmodel_meg <http://www.fieldtriptoolbox.org/tutorial/headmodel_meg>). 
> %% align the coordinate system
> load('standard_mri.mat'); % load mri data
> disp(mri)
> 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 = [];
> cfg.method='singleshell';
> 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
> figure;
> ft_plot_sens(grad, 'style', '*b');
> hold on
> ft_plot_vol(vol);
> while aligning the coordinate system I have chosen fiducial points (naison, LPA and RPA) using the instruction given by http://neuroimage.usc.edu/brainstorm/CoordinateSystems <http://neuroimage.usc.edu/brainstorm/CoordinateSystems>.
> 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 regard.  
> Thanks and Regards,
> Susmita Sen
> Research Scholar
> Audio and Bio Signal Processing Lab.
> E & ECE Dept.
> IIT Kharagpur
> <vol1.png><vol2.png><vol3.png>_______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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