<div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>Hi Jan-Mathias!</div><div><br></div><div>Thank you for the answer!</div><div>I changed the units of gradiometers and head model to cm. <br></div><div>This clearly decreased the residual variances. <br></div><div>Also, singleshell seems to work better than localspheres. <br></div><div><br></div><div>However, the transformation seems to still increase the residual variance a lot. </div><div><br></div><div>Here are some examples:<br></div><div>original -> template RV 407.64 %<br>original -> original RV 9.85 %<br>original -> template -> original RV 10.75 %<br>realigning trial 706<br>original -> template RV 393.13 %<br>original -> original RV 9.00 %<br>original -> template -> original RV 9.90 %<br>realigning trial 707<br>original -> template RV 362.10 %<br>original -> original RV 8.33 %<br>original -> template -> original RV 9.18 %<br>realigning trial 708<br>original -> template RV 377.15 %<br>original -> original RV 9.43 %<br>original -> template -> original RV 10.33 %<br></div><div><br></div><div>The code is now as follows:</div><div>load([data_path nameList{subj} '.mat']);<br>grad = datafinal.grad;<br>hs=ft_read_headshape([hdr_path nameList{subj} '/hs_file']);<br> <br></div><div>cfg = [];<br>cfg.method = 'singlesphere';<br>cfg.geom = hs;<br>cfg.grad = grad;<br>cfg.feedback = true;<br>vol = ft_prepare_headmodel(cfg);<br><br>vol = ft_convert_units(vol,'cm');<br>grad = ft_convert_units(grad,'cm');<br>cfg = [];<br>cfg.template = template;<br>cfg.inwardshift = 2.5;<br>cfg.feedback ='no';<br>cfg.vol = vol;<br>data = ft_megrealign(cfg, data);<br></div><div><br></div><div>Best,</div><div>Maria<br></div></div></div></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr">to 1. marrask. 2018 klo 10.35 Schoffelen, J.M. (Jan Mathijs) (<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>) kirjoitti:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Hi Maria,
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<div>Are you sure about the units in your headmodel (and gradiometers)? Using the value 1.0 as an inwardshift parameter suggests ‘cm’. Not sure what will happen when by accident the hs_file is in ‘m’ (which, as far as I know, is usually the case).</div>
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<div>Best wishes,</div>
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<div>Jan-Mathijs</div>
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J.M.Schoffelen, MD PhD<br>
Senior Researcher, VIDI-fellow - PI, language in interaction<br>
Telephone: +31-24-3614793</div>
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Physical location: room 00.028</div>
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Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br>
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<div>On 29 Oct 2018, at 13:33, Maria Hakonen <<a href="mailto:maria.hakonen@gmail.com" target="_blank">maria.hakonen@gmail.com</a>> wrote:</div>
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<div dir="ltr">Dear FieldTrip experts,
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<div>I have run ft_mergealign across subjects to align the head positions. However, the residual variance between the original and the realigned data seems to be high:</div>
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<div>original -> template RV 21232.46 %</div>
<div>original -> original RV 36.96 %</div>
<div>original -> template -> original RV 9579.95 %</div>
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<div>Could someone please let me know what would be the largest acceptable change in the residual variance, and what should I do if the residual variance is too high? Does the increase in residual variance mean that there is a large shift in the head
position? </div>
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<div>I have used ft_mergealign as follows:</div>
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<div>template = list of subjects (i.e. I want to calculate an average head position over the subjects)</div>
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<div>grad = data.grad;</div>
<div>hs=ft_read_headshape([hdr_path nameList{subj} '/hs_file']);</div>
<div>vol = ft_headmodel_localspheres(hs,grad);</div>
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<div>cfg = [];</div>
<div>cfg.template = template;</div>
<div>cfg.inwardshift = 1.0;</div>
<div>cfg.vol = vol;</div>
<div>data_aligned = ft_megrealign(cfg, data);</div>
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<div>Best,</div>
<div>Maria <br>
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