[FieldTrip] Assistance with digitized electrodes and individual MRI alignment for EEG source analysis

[Enrico Sozza]

Dear FieldTrip Community,

I am writing from the University of Barcelona, attempting to implement EEG source reconstruction methods in my PhD project.
I am experiencing some issues that neither the tutorials themselves nor the FAQs seem to help troubleshooting. I am therefore reaching out seeking for some useful hints or users that faced and overcame similar problems.

What I am trying to do:
source localizing EEG activity through beamforming (DICS) making use of digitized 3D electrodes location (Polhemus Fastrak) co-registered with individual MRI.

What issues I am experiencing:


  1.
alignment of the individual MRI to a common coordinate system using fieldtrip function: using ft_volumerealing and manually marking relevant landmarks seem to effectively generate a transformation matrix and produce a partially aligned output; however, when I check the quality of the alignment, I can still see the head twisted (transversal view), reflecting (I assume) the position of the head in the scan. This twisting seems to be normalized only by ft_volumereslice, which however inclines forward the MRI in the sagittal view.
Why does this happen? Isn't the realignment step supposed adjust rotation and any other geometrical positioning related issues? Can we avoid the forward inclination produced by ft_volumereslice while still obtaining isometric voxels?
here's the code I used (note that it doesn't matter which landmarks and coord sys I choose, the problem persists)
     *
cfg          = [];
cfg.method   = 'interactive';
cfg.coordsys = 'ctf';
mri_aligned_fiducials = ft_volumerealign(cfg, mri);

  2.
Alignement affination with head shape of the subject: as suggested by some tutorials (i.e., https://www.fieldtriptoolbox.org/workshop/oslo2019/forward_modeling/)  I am trying to refine the alignment of the individual MRI (in order to improve the later co-registration with the electrodes) using the head shape points of the subject collected through the Polhemus. However, when I try this alignment, the head shape defined by the collected head points results way bigger and disproportioned as compared to the head shape generated by fieldtrip from the subject's MRI (I guess it'd correspond to the mesh of the scalp). Likewise, the position of the fiducials (e.g., nasion, l/r tragus) results challengingly inconsistent. This problem shows up also when later on I try to co-register the electrodes with the triangulated mesh of the scalp based on fiducials or manually, which as you can imagine does not provide a reliable accuracy. It seems the only way to overcome this aspect is changing the scaling of the MRI in the manual adjustment, which however leads to a loss in proportion consistency between x, y and z. Any idea of why this happens and how to find an effective solution? Here's the codes I tried to use

           
           % Alignment of MRI to headshape
cfg                                       = [];
cfg.method                              = 'headshape';
cfg.headshape.headshape        = head;
cfg.coordsys                         = 'ctf';
cfg.headshape.icp                 = 'no';  % (automatic iteration leads to catastrophic results)
mri_aligned_headshape               = ft_volumerealign(cfg, mri_aligned_fiducials);

% Alignment of elec with headmodel based on fiducials (nasion, lpa and rpa - which are actually left and right traguses in both structures)
cfg           = [];
cfg.method     = 'fiducial';
cfg.target      = elec_mri; % ( this are manually pointed fiducials from the 'mri_realinged_headshape'
cfg.elec             = elec;
cfg.fiducial      = {'NAS', 'LPA', 'RPA'};
cfg.feedback = 'yes';
elec_realigned       = ft_electroderealign(cfg);


  1.  Relevant artifacts on the headmodel scalp mesh: many of the individual MRIs I am using are collected with the subject wearing digital goggles (part of active tasks fMRI sessions). Therefore, when I compute segmentation and mesh for the headmodel, the goggle shape results embedded in the scalp mesh. May you know if this can cause issue with the later on computation of the forward model and of the inverse solution, although there are not electrodes placed on the goggle area? Actually I would need to exclude from the analysis the inferior and lateral electrodes, but it seems to me a more straighforward solution than using ft_defacevolume or ft_defacemesh, which based on my experience are flawly, not user-friendly, subjected to many errors and notsistematic (likewise for correcting parameters as cfg.scalpthreshold or cfg.scalpsmooth in ft_volumesegment).

If the answer to my question is yes, how would you suggest to troubleshoot the issue? Would it be better for me to use other MRI processing tools to exclude goggles with a more efficient mask setting (e.g., manual drawing)?


I've been struggling for a while already, so that I would really appreciate any type of suggestion, a direct solution or  sources I can consult, whichever they may be!


Your time and attention are very much appreciated.

Best of luck with your work,

Regards


Enrico Sozza, PhD Student

Brainlab – Cognitive Neuroscience Research Group

Department of Clinical Psychology and Psychobiology

Institute of Neurosciences

University of Barcelona

P. Vall d'Hebron 171, 08035 Barcelona, Catalonia-Spain
Tel: +34 933 125 058 – Fax: +24 934 021 584

http://www.ub.edu/brainlab

http://www.neurociencies.ub.edu<http://www.neurociencies.ub.edu/>


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