[FieldTrip] Regarding headmodel construction

[Simon Homolle]

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 <mailto: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','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 <mailto: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);
>> 
>> %% 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 <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 <mailto:fieldtrip at donders.ru.nl>
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip <https://mailman.science.ru.nl/mailman/listinfo/fieldtrip>
> 
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