[FieldTrip] Electrode alignment to standard MRI template

[Annika Thierfelder]

Hello everyone,

short update on my question, that is maybe easier to answer without 
going through the code itself.

I believe that the heart of the problem lies (of course) in the 
coordinate definitions of the electrodes and the MRI. So, I experimented 
a little with the example electrode set that is aligned to the standard 
BEM model that results from the standard MRI. If I try to align the 
example electrodes to the MRI (which is not necessary but it also should 
not hurt), I discovered that I get the same shift into the z-direction 
for the example electrodes.

So, the basic question underlying my problem would be: How can the MRI 
and the eletrodes be aligned if their fiducials are so different, they 
even seem to be in different coordinate systems? Shouldn't they be kind 
of similar if they are aligned? I did not see any further coordinate 
transformation in the BEM computation from the MRI (except for the 
conversion into 'acpc' in ft_volumesegment which doesn't change 
anything) that would explain the alignment later on.

MRI fiducials:
NAS [1, 0, 0]
LPA [0, 83, 0]
RPA [0, -117, 0]

template electrode fiducials are roughly:
NAS [0, 87, -40]
LPA [-86, -20, -48]
RPA [86, -20, -48]

Also, the MRI is supposed to be in MNI coordinates, which I don't 
understand why, because already the first dimension doesn't point to the 
right. I feel like understanding why the coordinates are this way would 
be a crucial step to solve my problem.

I'm very thankful for any help on this problem. If I understand this, I 
hopefully can figure out the rest myself.

Best regards,
Annika

On 8/21/2018 6:21 PM, Annika Thierfelder wrote:
> Hello everyone,
>
> I started using fieldtrip last week to do EEG source analysis and I 
> experienced some issues when trying to align the EEG to the MRI. Since 
> we don't have MRI scans for our subjects, I used the standard_mri from 
> the template folder.
>
> The solution that works "best" until now is to align the electrodes 
> with the MRI fiducials and compute the BEM from the MRI seperately (I 
> used bemcp for that since I work on windows, so dipoli doesn't run). 
> However, when I plot the aligned electrodes together with the BEM head 
> surface, the electrodes are in the correct orientation but they have 
> an offset along the z-axis. I put the code I used below and uploaded 
> the picture of the electrodes and the head model on google drive: 
> https://drive.google.com/open?id=1b7Q3YGWGyzaa5oXeE-PfOOHNIDoFaLO1
>
> There are two things I'm wondering about now:
>
> Why are the nasion head coordinates in the MRI template [1, 0, 0] and 
> not [100, 0, 0], which would make more sense (at least in my opinion) 
> since the units are in mm and I thought the nasion is not supposed to 
> be inside the head? The LPA and RPA values are [0, 83, 0] and [0, 
> -117, 0] respectively, which seems perfectly fine to me.
>
> I have the feeling that the problem arises because the two coordinate 
> systems of the data do not have the same origin. Can I shift the 
> coordinate system of the electrode space before aligning them? I only 
> found ways how to change the coordinate system of the MRI. I also 
> tried to change the MRI coordinate system first before aligning the 
> electrodes, but I found that I cannot create the BEM model with 
> 'bemcp' anymore. It seems to throw an error if I give it an MRI with 
> any coordinate system that is not 'spm'. So I kind of have the feeling 
> that I need to get the electrodes into the 'spm' coordinates to match 
> the MRI and BEM head.
>
> Thank you a lot in advance for your support!
>
> Annika
>
> PS: I know there has been a similar problem once in this mailing list, 
> but I checked the suggestions and they did not work for me, also it 
> seemed as if in the end it came down to fitting the electrodes 
> manually there, and I suppose there can be another solution for this.
>
> ================================================================================== 
>
>
> Code for the electrode alignment:
>
> %This is my how my electrode data looks like:
> disp(chanlocs_124)
>       label: {124×1 cell}
>     elecpos: [124×3 double]
>        unit: 'mm'
>
> % get fiducials from the MRI template
> vox_Nas = mri_spm.hdr.fiducial.mri.nas;
> vox_Lpa = mri_spm.hdr.fiducial.mri.lpa;
> vox_Rpa = mri_spm.hdr.fiducial.mri.rpa;
>
> % I know I can skip this step because I can directly use the 
> head-coordinates given in the MRI template
> % I kept it because it doesn't make a difference
> vox2head = mri_spm.hdr.transformMRI2Head;
> head_Nas = ft_warp_apply(vox2head, vox_Nas, 'homogeneous'); % nasion
> head_Lpa = ft_warp_apply(vox2head, vox_Lpa, 'homogeneous'); % Left 
> preauricular
> head_Rpa = ft_warp_apply(vox2head, vox_Rpa, 'homogeneous'); % Right 
> preauricular
>
> % save the MRI fiducials as target structure for the realignment
> % in our data set, the LPA is named TTP9 and the RPA is TTP10, so I 
> renamed them
> elec_mri.elecpos(1,:) = head_Nas;
> elec_mri.elecpos(2,:) = head_Lpa;
> elec_mri.elecpos(3,:) = head_Rpa;
> elec_mri.label = {'Nz', 'TTP9', 'TTP10'};
> elec_mri.unit  = 'mm';
>
> % coregister the electrodes to the MRI using fiducials
> cfg = [];
> cfg.method   = 'fiducial';
> cfg.target   = elec_mri;
> cfg.elec     = chanlocs_124;
> cfg.fiducial = {'Nz', 'TTP9', 'TTP10'};
> chanlocs_124_spm = ft_electroderealign(cfg);
>
> =================================================================================================== 
>
> Just in case this is also of interest, this is how I compute the BEM 
> headmodel from the same MRI template:
>
> % segments the MRI into three different tissue parts
> % creates binary masks for each point and tissue part
> cfg = [];
> cfg.output    = {'brain','skull','scalp'};
> segmented_mri  = ft_volumesegment(cfg, mri_spm);
>
> %% create mesh with different tissues
> cfg=[];
> cfg.tissue={'brain','skull','scalp'};
> cfg.numvertices = [3000 2000 1000];
> bnd=ft_prepare_mesh(cfg,segmented_mri);
>
> % compute headmodel
> cfg        = [];
> cfg.tissue={'brain','skull','scalp'};
> cfg.method ='bemcp';
> vol        = ft_prepare_headmodel(cfg, bnd);
>
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> https://doi.org/10.1371/journal.pcbi.1002202