[FieldTrip] Creating head model using template MRI

[Maria Hakonen]

Dear Fieldtrip experts,


I would like to run ft_sourceanalysis as shown in the Appendix 1 here:
http://www.fieldtriptoolbox.org/tutorial/coherence


ft_sourceanalysis requires head model as a parameter.  I don’t have mri
images for my MEG subjects (measured with 306 channel Elekta Neuromag
system) and, therefore, I would need to use a template head model or a
template MRI. I think that I should use a local spheres volume conduction
model as suggested here:
http://www.fieldtriptoolbox.org/tutorial/headmodel_meg.


Could someone please let me know if standard_mri.mat is the file that I
should use?


I created a head model using standard_mri.mat and following the
instructions here: http://www.fieldtriptoolbox.org/tutorial/headmodel_meg


I first created the head model for the example data and checked whether I
can get the same result as in the example (Appendix 1:
http://www.fieldtriptoolbox.org/tutorial/coherence).


However, the result doesn’t seem to be correct:


​


Could someone please let me know what I am doing wrong?


Many thanks already in advance if you can help!


Best,

Maria


Here is the scrip that I have tested:

hdr = ft_read_header('
C:\Users\Maria\Documents\filedtrip\fieldtrip-20170620\SubjectCMC.ds');

grad = hdr.grad;

load('standard_mri.mat');

load('freq.mat')



cfg           = [];

cfg.output    = 'brain';

segmentedmri  = ft_volumesegment(cfg, mri);



cfg                       = [];

cfg.grad                  = hdr.grad;

cfg.feedback              = false;

cfg.method                = 'localspheres';

vol                       = ft_prepare_headmodel(cfg,segmentedmri);



cfg = [];

mri = ft_volumereslice(cfg, mri);



cfg                 = [];

cfg.method          = 'dics';

cfg.refchan         = 'EMGlft';

cfg.frequency       = 18;

cfg.hdmfile         = vol;

cfg.inwardshift     = 1;

cfg.grid.resolution = 1;

cfg.grid.unit       = 'cm';

source              = ft_sourceanalysis(cfg, freq);



cfg            = [];

cfg.parameter  = 'coh';

cfg.downsample = 2;

interp         = ft_sourceinterpolate(cfg, source, mri);



cfg              = [];

cfg.method       = 'ortho';

cfg.interactive  = 'yes';

cfg.funparameter = 'coh';

figure; ft_sourceplot(cfg, interp);
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