[FieldTrip] Regarding headmodel construction

[Susmita Sen]

Dear Simon,

Thanks a lot for your suggestion.

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

On Mon, Oct 3, 2016 at 6:48 PM, Simon Homolle <s.homolle at donders.ru.nl>
wrote:

> Dear Susmita,
>
> I think first all
> http://www.fieldtriptoolbox.org/faq/how_are_the_different_
> head_and_mri_coordinate_systems_defined
> is a nice place to go to understand the different coordinate systems.
>
> I’m not to well aware about the Yokogawa coordinate system, but my first
> expectation would be that this coordinate systems is shifted lower than the
> CTF. After aligning with the different coordinate systems you should look
> at mri_aligned.coordsys
>
> 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 03 Oct 2016, at 14:59, Susmita Sen <susmitasen.ece at gmail.com> wrote:
>
> 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.o
>> rg/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>______________________________
>> _________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
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>
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