[FieldTrip] fieldtrip Digest, Vol 36, Issue 16

[Nicola Molinaro]

Dear Hanneke,
this is exactly what I did, however, for better exploring the possibilities
I also added an extra z point:

lpa                = [187.46   179.33   153.30];
nas                = [127.59   147.10   244.07];
rpa                = [ 69.76   185.61   147.85];
zpoint             = [ 99.19    83.57   132.39];

and running ft_volumerealign with 'fiducials'

everything calculated in voxel coordinates and since I was curiously biased
by this webpage (outdated maybe but did not find anything updated):

http://fieldtrip.fcdonders.nl/example/read_neuromag_mri_and_create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space

I tried to switch a little bit the coordinates exchanging 'y' and 'x' (and
it does not work) and exchanging lpa and rpa (I should have the zpoint that
saves me anyway).

When I plot all these points with the MEG channel's coordinates and the
brain volume:

vol = ft_convert_units(vol,'cm');
mri_real = ft_convert_units(mri_real,'cm');
hs=ft_read_headshape('<filename>.fif', 'unit','cm'); %get headshape points
ft_plot_vol(vol)
ft_plot_headshape(hs)
hold
plot3(hs.fid.pnt(:,1),hs.fid.pnt(:,2),hs.fid.pnt(:,3),'b+')
plot3(DATA.grad.chanpos(:,1),DATA.grad.chanpos(:,2),DATA.grad.chanpos(:,3),'k*')

everything seems perfect independently from switching lpa and rpa. However,
after source reconstruction, when I interpolate

cfg=[];
cfg.parameter='avg.pow';
inter_lcmv=ft_sourceinterpolate(cfg, lcmvdiff, mri_real);

and plot my data

cfg               = [];
cfg.method        = 'slice';
cfg.coordsys      = 'neuromag';
cfg.funparameter  = 'avg.pow';
cfg.maskparameter = cfg.funparameter;
cfg.funcolorlim   = [4 10];
cfg.opacitylim    = [4 10];
cfg.opacitymap    = 'rampup';
ft_sourceplot(cfg,inter_lcmv);

everything changes (unpredictably) depending on the coordinates of the lpa
and rpa. I suspect there is something about ft_sourceinterpolate
and ft_sourceplot I don't control.

Actually, I tried also doing fine-grained realignment also with the
headshape points as suggested by Jan (pretty slow ft_volumerealign with
method headshape and isotrack points read form a .fif file).

A part that realignment was not really nice (maybe because we took many
isotrack points along the nose), ft_sourceplot gave new different results...

Now I am kind of lost.

Nicola







> Message: 1
> Date: Tue, 12 Nov 2013 10:28:33 +0000
> From: <Hanneke.vanDijk at med.uni-duesseldorf.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] [Fieldtrip] question about coregistration
> Message-ID:
>         <495873C58A622E45A3ABF4813B9451EC6E3EF242 at MAIL3-UKD.VMED.UKD>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Nicola and Jan-Mathijs,
>
>
> A simple solution can also be to save the points (the fiducials) that you
> have collected in MRIlab in 'voxel'. After we do the realignment with the
> polhemus data, we delete all points. We then create points at the final
> fiducial locations and export these. In this 'Export points' window you can
> select if you want to save them in head or voxel coordinates. The resulting
> .txt files can be read in matlab, and you can use them to realign the MRI
> in fieldtrip.
>
> Good luck!
>
> Thanks for the info as well, Jan-Mathijs! I didn't know about the two step
> solution in Fieldtrip, but will certainly give it a try!
>
> Groetjes Hanneke
>
>
> __________________________________________
>
> Hanneke van Dijk, PhD
>
> http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html
> Institute for Clinical Neuroscience,
> Heinrich Heine Universit?t D?sseldorf, Germany
> Hanneke.vanDijk at med.uni-duesseldorf.de<mailto:
> Hanneke.vanDijk at med.uni-duesseldorf.de>
> Tel. +49 (0) 211 81 13074
> __________________________________________
>
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------------------------------
Nicola Molinaro, Phd
Staff Scientist
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
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