[FieldTrip] Regarding headmodel construction

[Susmita Sen]

Dear Simon,

Thank you very much for your response. I am sorry to bother you once
again with my doubt. The headmodel that I have constructed, has a flat
surface at the bottom. I would like to ask you to explain why that is
happening. If I use 'ctf' instead of 'yokogawa', the heamodel does not look
like this. I am attaching a file comparing these two headmodels. I have
circled some part of the figure which actually raises the question of
whether I am doing it correctly or not. Is there anything wrong in choosing
the fiducial points? Thank you in anticipation.

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

On Mon, Oct 3, 2016 at 1:49 PM, Simon Homolle <s.homolle at donders.ru.nl>
wrote:

> 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','i
> ndexed');
>
>
> 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/fieldt
> rip/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
> ).
>
> %% 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);
>
> %% SEGMENTATION
> 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.
>
> 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>______________________________
> _________________
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>
>
>
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