<div dir="ltr"><div>Dear Hanneke,</div><div>this is exactly what I did, however, for better exploring the possibilities I also added an extra z point:</div><div><br></div><div><div>lpa = [187.46 179.33 153.30];</div>
<div>nas = [127.59 147.10 244.07];</div><div>rpa = [ 69.76 185.61 147.85];</div><div>zpoint = [ 99.19 83.57 132.39];</div></div><div><br></div><div>and running ft_volumerealign with 'fiducials'</div>
<div><br></div><div>everything calculated in voxel coordinates and since I was curiously biased by this webpage (outdated maybe but did not find anything updated):</div><div><br></div><div><a href="http://fieldtrip.fcdonders.nl/example/read_neuromag_mri_and_create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space">http://fieldtrip.fcdonders.nl/example/read_neuromag_mri_and_create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space</a><br>
</div><div><br></div><div>I tried to switch a little bit the coordinates exchanging 'y' and 'x' (and it does not work) and exchanging lpa and rpa (I should have the zpoint that saves me anyway).</div><div>
<br></div><div>When I plot all these points with the MEG channel's coordinates and the brain volume:</div><div><br></div><div><div>vol = ft_convert_units(vol,'cm'); </div><div>mri_real = ft_convert_units(mri_real,'cm'); </div>
<div>hs=ft_read_headshape('<filename>.fif', 'unit','cm'); %get headshape points</div><div>ft_plot_vol(vol)</div><div>ft_plot_headshape(hs)</div><div>hold</div><div>plot3(hs.fid.pnt(:,1),hs.fid.pnt(:,2),hs.fid.pnt(:,3),'b+')</div>
<div>plot3(DATA.grad.chanpos(:,1),DATA.grad.chanpos(:,2),DATA.grad.chanpos(:,3),'k*')</div></div><div><br></div><div>everything seems perfect independently from switching lpa and rpa. However, after source reconstruction, when I interpolate</div>
<div><br></div><div><div>cfg=[];</div><div>cfg.parameter='avg.pow';</div><div>inter_lcmv=ft_sourceinterpolate(cfg, lcmvdiff, mri_real);</div></div><div><br></div><div>and plot my data</div><div><br></div><div><div>
cfg = [];</div><div>cfg.method = 'slice';</div><div>cfg.coordsys = 'neuromag';</div><div>cfg.funparameter = 'avg.pow';</div><div>cfg.maskparameter = cfg.funparameter;</div>
<div>cfg.funcolorlim = [4 10];</div><div>cfg.opacitylim = [4 10]; </div><div>cfg.opacitymap = 'rampup'; </div><div>ft_sourceplot(cfg,inter_lcmv);</div></div><div><br></div><div>everything changes (unpredictably) depending on the coordinates of the lpa and rpa. I suspect there is something about ft_sourceinterpolate</div>
<div>and ft_sourceplot I don't control.</div><div><br></div><div>Actually, I tried also doing fine-grained realignment also with the headshape points as suggested by Jan (pretty slow ft_volumerealign with method headshape and isotrack points read form a .fif file).</div>
<div><br></div><div>A part that realignment was not really nice (maybe because we took many isotrack points along the nose), ft_sourceplot gave new different results...</div><div><br></div><div>Now I am kind of lost.</div>
<div><br></div><div>Nicola</div><div><br></div><div><br></div><div><br></div><div> </div><div><br></div><div><br></div><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<br>
Message: 1<br>
Date: Tue, 12 Nov 2013 10:28:33 +0000<br>
From: <<a href="mailto:Hanneke.vanDijk@med.uni-duesseldorf.de">Hanneke.vanDijk@med.uni-duesseldorf.de</a>><br>
To: <<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
Subject: Re: [FieldTrip] [Fieldtrip] question about coregistration<br>
Message-ID:<br>
<495873C58A622E45A3ABF4813B9451EC6E3EF242@MAIL3-UKD.VMED.UKD><br>
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<br>
Hi Nicola and Jan-Mathijs,<br>
<br>
<br>
A simple solution can also be to save the points (the fiducials) that you have collected in MRIlab in 'voxel'. After we do the realignment with the polhemus data, we delete all points. We then create points at the final fiducial locations and export these. In this 'Export points' window you can select if you want to save them in head or voxel coordinates. The resulting .txt files can be read in matlab, and you can use them to realign the MRI in fieldtrip.<br>
<br>
Good luck!<br>
<br>
Thanks for the info as well, Jan-Mathijs! I didn't know about the two step solution in Fieldtrip, but will certainly give it a try!<br>
<br>
Groetjes Hanneke<br>
<br>
<br>
__________________________________________<br>
<br>
Hanneke van Dijk, PhD<br>
<a href="http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html" target="_blank">http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html</a><br>
Institute for Clinical Neuroscience,<br>
Heinrich Heine Universit?t D?sseldorf, Germany<br>
<a href="mailto:Hanneke.vanDijk@med.uni-duesseldorf.de">Hanneke.vanDijk@med.uni-duesseldorf.de</a><mailto:<a href="mailto:Hanneke.vanDijk@med.uni-duesseldorf.de">Hanneke.vanDijk@med.uni-duesseldorf.de</a>><br>
Tel. <a href="tel:%2B49%20%280%29%20211%2081%2013074" value="+492118113074">+49 (0) 211 81 13074</a><br>
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</blockquote><div><br></div><div> </div></div><div dir="ltr"><font color="#888888"><div><div style="color:rgb(34,34,34);font-family:arial;font-size:small">------------------------------</div><div style="color:rgb(34,34,34);font-family:arial;font-size:small">
Nicola Molinaro, Phd</div><div style="color:rgb(34,34,34);font-family:arial;font-size:small">Staff Scientist</div><div style="color:rgb(34,34,34);font-family:arial;font-size:small"><a href="http://www.bcbl.eu" target="_blank">www.bcbl.eu</a></div>
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