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<p class="MsoNormal"><span lang="EN-GB">Dear fieldtrippers, <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">I am struggling with aligning the individual MRI, the headmodel and electrode positions(EEG) for some days now, without any success.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">I would appreciate some help. <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">To begin with, as an input I have the subject specific MRI which was segmented with the use of freesurfer and MNE software.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">I load first the MRI ,the triangulated meshes for brain skull and skin, and the electrodes positions of 65-channel EEG.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">I am then computing the bem headmodel from the brain skull skin (computed with the use of MNE software)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Afterwards I am aligning the MRI to my headmodel (ft_volumerealign) and then I identify the fiducials with the interactive mode (ft_volumerealign).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">I do the transformation of the fiducial points with ft_warp_apply to the coordinates specified at the alignment.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Then I call the ft_electroderealign to align my electrodes to the mri’s fiducial points.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">And then I realign my electrodes manually.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">The problem is that no matter how much rotation translation scaling I do, it’s IMPOSSIBLE TO FIT THE ELECTRODES TO THE HEADMODEL!<br>
<br>
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">I tried the volume_realign with ctf coordinates as well and I tried the ft_electroderalign with the interactive mode only(without matching the fiducials), it doesn’t work.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Below you can find the code that I used. <o:p>
</o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Any ideas on this issue would be of great help!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">%% READ <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">% read mri <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">mri=ft_read_mri([freesurferDir 'mri\orig.mgz']);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">mri.coordsys='neuromag';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">% read surfaces <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">brain=ft_read_headshape([freesurferDir 'bem\brain.surf\Pilot08_brain_surface']);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">skull=ft_read_headshape([freesurferDir 'bem\brain.surf\Pilot08_inner_skull_surface' ]);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">skin=ft_read_headshape([freesurferDir 'bem\brain.surfilot08_outer_skin_surface' ]);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">% read electrodes positions <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">elec_file=[datadir '\raw\M10.elc'];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">elec=ft_read_sens(elec_file );<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">elec.coordsys='neuromag';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">elec.label=upper(elec.label);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">%% HEADMODEL<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">%assign values of segmented surfaces <o:p>
</o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">geom(1).tri=brain.tri;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">geom(2).tri=skull.tri;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">geom(3).tri=skin.tri;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">geom(1).pnt=brain.pnt;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">geom(2).pnt=skull.pnt;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">geom(3).pnt=skin.pnt;<o:p></o:p></span></p>
<p class="MsoNormal">% compute headmodel<o:p></o:p></p>
<p class="MsoNormal">vol=ft_headmodel_bemcp(geom);<o:p></o:p></p>
<p class="MsoNormal">vol=ft_convert_units(vol, 'mm');<o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-GB">vol.coordsys='neuromag';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">%% ALIGNMENTS <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">%align mri and headshape <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">mri_coord=ft_determine_coordsys(mri, 'interactive', 'yes');<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">vol_coord=ft_determine_coordsys(vol, 'interactive', 'yes');<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg=[];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg.method = 'headshape';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg.headshape=vol_coord.bnd(3);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">mri_headshape=ft_volumerealign(cfg,mri_coord);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">%find fiducials<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg=[];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg.method='interactive';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg.coordsys='neuromag';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">mri_fid=ft_volumerealign(cfg,mri_headshape);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">%% APPLY TRANSFORMATIONS ON FIDUCIALS<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">transm=mri_fid.transform;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">nas=ft_warp_apply(transm,mri_fid.cfg.fiducial.nas, 'homogenous');<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">lpa=ft_warp_apply(transm,mri_fid.cfg.fiducial.rpa, 'homogenous');<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">rpa=ft_warp_apply(transm,mri_fid.cfg.fiducial.lpa, 'homogenous');<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="FR">fid.chanpos = [nas; rpa; lpa]; <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">fid.elecpos =fid.chanpos;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">fid.label = {'NASION', 'RIGHTEAR','LEFTEAR'}; % same labels as in elec<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">fid.unit = 'mm'; % same units as mri<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">% Automatic electrode alignment using the fiducials
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg.method = 'fiducial';
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg.template = fid;
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg.elec = elec;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg.fiducial = {'NASION', 'RIGHTEAR','LEFTEAR'}; % labels of fiducials in fid and in sens<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg.headshape=vol_coord.bnd(3); % use the scalp as headshape<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">elec_aligned_fid = ft_electroderealign(cfg);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">%% Interactive alignment of electrodes to fix some misalignment<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg=[];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg.method='interactive';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg.elec=elec_aligned_fid;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">cfg.headshape=vol_coord.bnd(3); % use the scalp as headshape<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">elec_aligned=ft_electroderealign(cfg);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Best Regards, <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black;mso-fareast-language:NL">K. (Nadia) Kalogianni</span></b><span lang="EN-GB" style="font-family:"Tahoma","sans-serif";color:black;mso-fareast-language:NL"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black;mso-fareast-language:NL">PhD candidate</span><span lang="EN-GB" style="font-family:"Tahoma","sans-serif";color:black;mso-fareast-language:NL"><o:p></o:p></span></p>
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