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<p class="MsoNormal"><span style="font-size:10.0pt">Hi Alex,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt">I believe there might be an issue with the logic you're using.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt">You move the three fiducials from the headshape space to the MRI space. Subsequently you define the MRI coordinate system based on these three fiducials. However, that does not guarantee that your transformed
headshape fiducials correspond to the actual nasion, LPA, and RPA in the MRI space. You can plot
</span><span style="font-size:10.0pt">nas_voxel_mriread, lpa_voxel_mriread, rpa_voxel_mriread together with your MRI to see if these points correspond to the actual</span><span style="font-size:10.0pt"> nasion, LPA, and RPA in the MRI space.</span><span style="font-size:10.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt">I suggest you first define the fiducials directly in the MRI space using ft_volumerealign with cfg.method = 'interactive'. Once you've done that, you'll
<b>have three points in the MRI space </b>and three corresponding points in the head shape which you can then co-register.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt">Best regards,<br>
Konstantinos<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> fieldtrip <fieldtrip-bounces@science.ru.nl>
<b>On Behalf Of </b>Alex Williams via fieldtrip<br>
<b>Sent:</b> Thursday, November 14, 2024 7:26 PM<br>
<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Cc:</b> Alex Williams <alexanderwil2024@my.fit.edu><br>
<b>Subject:</b> [FieldTrip] Registration of neuromag data<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi there FieldTrip community,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> 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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> 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. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Here is the code I used for coregistration to acquire the image above:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#008013">%% Realign Coord Sys.</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#0E00FF">function
</span><span style="font-size:10.0pt;font-family:Consolas">mrialign=coregistration(Path1,Path2,mriread,S,job)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">addpath <span style="color:#A709F5">
/Users/alexanderwil2024/MATLAB-Drive/Research/MATLAB code/Beamformer Pipeline</span><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg=[];<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">headshape=ft_read_headshape([Path1 Path2]);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">headshape=ft_convert_coordsys(headshape,<span style="color:#A709F5">'neuromag'</span>);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">vox2vox = inv(mriread.transform);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">nas_voxel_mriread = ft_warp_apply(vox2vox, headshape.fid.pos(2,:),
<span style="color:#A709F5">'homogenous'</span>); <span style="color:#008013">% nasion</span><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">lpa_voxel_mriread = ft_warp_apply(vox2vox, headshape.fid.pos(1,:),
<span style="color:#A709F5">'homogenous'</span>); <span style="color:#008013">% Left preauricular</span><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">rpa_voxel_mriread = ft_warp_apply(vox2vox, headshape.fid.pos(3,:),
<span style="color:#A709F5">'homogenous'</span>); <span style="color:#008013">% Right preauricular</span><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg=[];<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">nas1=nas_voxel_mriread;
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">lpa1=lpa_voxel_mriread;
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">rpa1=rpa_voxel_mriread;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.fiducial.nas=nas1;
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.fiducial.lpa=lpa1;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.fiducial.rpa=rpa1;
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.coordsys=<span style="color:#A709F5">'neuromag'</span>;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.method=<span style="color:#A709F5">'fiducial'</span>;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">mrialign = ft_volumerealign(cfg, mriread);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">ft_sourceplot([],mrialign);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg=[];<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.method=<span style="color:#A709F5">'headshape'</span>;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.spmversion=<span style="color:#A709F5">'spm12'</span>;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.headshape.headshape=headshape;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.headshape.interactive =
<span style="color:#A709F5">'no'</span>;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">mrialign=ft_volumerealign(cfg, mrialign);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#008013">% ********FOR VISUALIZING CO-REGISTRATION: IMPORTANT FOR FIDUCIALS!!!</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#008013">% cfg=[];</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#008013">% cfg.method='headshape';</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#008013">% cfg.spmversion='spm12';</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#008013">% cfg.headshape.headshape=headshape;</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#008013">% cfg.headshape.interactive = 'yes';</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#008013">% ft_volumerealign(cfg, mrialign);</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg=[];<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.parameter=<span style="color:#A709F5">'anatomy'</span>;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.filename=[<span style="color:#A709F5">'/Volumes/My Book/coreg_mri_niftis/mrialign '</span>,S,<span style="color:#A709F5">' for job '</span>,job];<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">cfg.filetype=<span style="color:#A709F5">'nifti'</span>;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">ft_volumewrite(cfg,mrialign);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">close <span style="color:#A709F5">
all</span><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas">o=1;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:#0E00FF">end</span><span style="font-size:10.0pt;font-family:Consolas"><o:p></o:p></span></p>
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<p class="MsoNormal"> 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:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><img width="542" height="493" style="width:5.65in;height:5.1333in" id="_x0000_i1027" src="cid:image001.png@01DB3752.9B4AD420"><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> 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:<br>
<br>
<img width="542" height="493" style="width:5.65in;height:5.1333in" id="Picture_x0020_2" src="cid:image002.png@01DB3752.9B4AD420"><br>
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:<br>
<br>
<img width="542" height="493" style="width:5.65in;height:5.1333in" id="Picture_x0020_1" src="cid:image003.png@01DB3752.9B4AD420"><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-Alex<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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