[FieldTrip] Registration of neuromag data

Fri Nov 15 15:48:35 CET 2024

Oh I see! I truly apologize for that. I didn't catch that you were
referring to the figure name in the image. Thanks so much again for
clarifying again. So figure 3 (i.e. the model with the sagittal tilt) uses
the inverted transform and then uses the resulting transformed fiducial
coordinates with volumerealign's fiducial method to obtain the coregistered
model within a neuromag coordinate system (mrialign). But then, it takes
that obtained mrialign variable and applies the volumerealign function once
more using the headshape method to obtain the model in figure 3. Due to
using volumerealign a second time using the headshape method after the
model is brought into neuromag space using the first volumerealign, would
the use of the second volumerealign in figure 3 be necessary? I only ask
because figure 4 (i.e. the model with a larger axial distance from the
sensor array) also uses the inverted transform but only uses the
volumerealign function once to apply the fiducials, completely eschewing
the use of the second volumerealign that applies a headshape method.

On Fri, Nov 15, 2024, 07:31 Schoffelen, J.M. (Jan Mathijs) via fieldtrip <
fieldtrip at science.ru.nl> wrote:

> Sorry if I was unclear Alex, with ‘figure 3’ I meant the first figure in
> your e-mail, i.e. the one which correctly uses the inverse of the
> transformation matrix, to express the fiducials in voxel coordinates, and
> then correctly updates the mri’s transformation matrix.
>
> Best wishes,
> Jan-Mathijs
>
>
> On 15 Nov 2024, at 13:13, Alex Williams <alexanderwil2024 at my.fit.edu>
> wrote:
>
> You don't often get email from alexanderwil2024 at my.fit.edu. Learn why
> this is important <https://aka.ms/LearnAboutSenderIdentification>
> Hi Jan-Mathijs,
>
>
>    Thanks so much for your response! So the third image uses both
> volumerealigns but uses a non-inverted transform from mriread. The only
> image that uses only one call to volumerealign applying the fiducial method
> is image two, but it applies an inverted transform from mriread. But was
> hoping to confirm that the third image would be the best for coregistration
> in this case.
>
> -Alex
>
>
>
> On Fri, Nov 15, 2024, 05:32 Schoffelen, J.M. (Jan Mathijs) via fieldtrip <
> fieldtrip at science.ru.nl> wrote:
>
>> Hi Alex,
>>
>> To be honest, I have the impression that what you plotted in ‘figure 3’
>> makes sense.
>>
>> The other ones don’t make sense, because the sensors are expressed in
>> neuromag space (I assume) so the ‘brain’ needs to be brought into neuromag
>> space as well, which is what you do with your first call to
>> ft_volumerealign. Unless I am missing something.
>>
>>
>> Best wishes,
>> Jan-Mathijs
>>
>> On 14 Nov 2024, at 19:26, Alex Williams via fieldtrip <
>> fieldtrip at science.ru.nl> wrote:
>>
>> Hi there FieldTrip community,
>>
>>   I was curious if anyone would be familiar with an issue I came across
>> within my study. I'm currently using an lcmv beamformer for source
>> reconstruction of several subjects within the CamCan data set using their
>> MEEG data. Right now, I'm currently looking back into the process of
>> coregistration once more. The meeg data and headshape data I have use
>> neuromag coordinates and I believe the coordinates of the fiducials are in
>> voxel-coordinates. For all of the subjects, I get a coregistered
>> orientation that seems to be tilted relative to the sensor array.
>>
>>  I'm unsure if this would be the correct orientation based on what I've
>> seen from previous head model orientations. However, since I'm unfamiliar
>> with how the head would be oriented within a neuromag system, I was
>> wondering if there was any way to confirm that this orientation would be
>> correct or if there may be something that needs to be rectified in the code
>> for proper orientation.
>>
>> Here is the code I used for coregistration to acquire the image above:
>>
>> %% Realign Coord Sys.
>> function mrialign=coregistration(Path1,Path2,mriread,S,job)
>> addpath /Users/alexanderwil2024/MATLAB-Drive/Research/MATLAB
>> code/Beamformer Pipeline
>> cfg=[];
>> headshape=ft_read_headshape([Path1 Path2]);
>> headshape=ft_convert_coordsys(headshape,'neuromag');
>> vox2vox = inv(mriread.transform);
>> nas_voxel_mriread = ft_warp_apply(vox2vox, headshape.fid.pos(2,:),
>> 'homogenous'); % nasion
>> lpa_voxel_mriread = ft_warp_apply(vox2vox, headshape.fid.pos(1,:),
>> 'homogenous'); % Left preauricular
>> rpa_voxel_mriread = ft_warp_apply(vox2vox, headshape.fid.pos(3,:),
>> 'homogenous'); % Right preauricular
>>
>> cfg=[];
>> nas1=nas_voxel_mriread;
>> lpa1=lpa_voxel_mriread;
>> rpa1=rpa_voxel_mriread;
>> cfg.fiducial.nas=nas1;
>> cfg.fiducial.lpa=lpa1;
>> cfg.fiducial.rpa=rpa1;
>> cfg.coordsys='neuromag';
>> cfg.method='fiducial';
>> mrialign = ft_volumerealign(cfg, mriread);
>> ft_sourceplot([],mrialign);
>>
>> cfg=[];
>> cfg.method='headshape';
>> cfg.spmversion='spm12';
>> cfg.headshape.headshape=headshape;
>> cfg.headshape.interactive = 'no';
>> mrialign=ft_volumerealign(cfg, mrialign);
>>
>> % ********FOR VISUALIZING CO-REGISTRATION: IMPORTANT FOR FIDUCIALS!!!
>> % cfg=[];
>> % cfg.method='headshape';
>> % cfg.spmversion='spm12';
>> % cfg.headshape.headshape=headshape;
>> % cfg.headshape.interactive = 'yes';
>> % ft_volumerealign(cfg, mrialign);
>>
>> cfg=[];
>> cfg.parameter='anatomy';
>> cfg.filename=['/Volumes/My Book/coreg_mri_niftis/mrialign ',S,' for job '
>> ,job];
>> cfg.filetype='nifti';
>> ft_volumewrite(cfg,mrialign);
>> close all
>> o=1;
>> end
>>   In this code, mriread refers to the subject's raw MRI nifti data after
>> being read in. tably, after the first use of volumerealign within the code
>> to apply the fiducials from the mri nifti (mrialign = ft_volumerealign(cfg,
>> mriread)), I use it again to apply a headshape-based method. I obtain this
>> sagitally tilted positioning when using this setup:
>>
>> <Both volumerealigns.png>
>>
>>   For additional reference, if I were to only use the first instance of
>> the volumerealign function to apply the fiducials to mriread without using
>> the second instance to apply the headshape method, I would obtain this
>> coregistered model, which seem properly oriented but slightly removed from
>> the sensor array:
>>
>> <Only fiducial volumerealign.png>
>>
>>
>
>> Additionally, the vox2vox transform matrix inverts mriread's transform
>> matrix to create the following coregistered positions. However, when the
>> vox2vox transform doesn't use the inverted transform (vox2vox
>> =mriread.transform) and applies the full code with both
>> volumerealign methods, it leads to a coronally tilted positioning:
>>
>> <image.png>
>>
>>
>>
>> -Alex
>>
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