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</o:shapelayout></xml><![endif]--></head><body lang=DE link="#0563C1" vlink="#954F72"><div class=WordSection1><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span lang=EN-US>Dear fieldtrip users, <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I have two simple questions about constructing an individual head model that keep me puzzling.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span lang=EN-US><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span lang=EN-US>I get a warning when using cfg.method = 'singleshell';<o:p></o:p></span></p><p class=MsoNormal style='text-indent:35.4pt'><span lang=EN-US>The warning is: <span style='color:red'>Warning: please specify cfg.method='projectmesh', 'iso2mesh' or 'isosurface'<o:p></o:p></span></span></p><p class=MsoNormal style='margin-left:70.8pt;text-indent:35.4pt'><span lang=EN-US style='color:red'>> In ft_prepare_mesh at 138<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:red'> In ft_prepare_headmodel at 344 <o:p></o:p></span></p><p class=MsoNormal style='margin-left:70.8pt;text-indent:35.4pt'><span lang=EN-US style='color:red'>Warning: using 'projectmesh' as default<o:p></o:p></span></p><p class=MsoNormal style='text-indent:35.4pt'><span lang=EN-US>I checked the cfg.method in the reference documentation as well as in the manuals on the fieldtrip website and here it is used as well. Does anyone have an idea why I can’t use it? <o:p></o:p></span></p><p class=MsoListParagraph><span lang=EN-US>My full code is: <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> cfg = [];<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> cfg.method = 'singleshell';<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> hdm = ft_prepare_headmodel(cfg, seg);<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><strong><span lang=EN-US style='font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> </span></span></span></strong><![endif]><span lang=EN-US> when plotting the <strong><span style='font-family:"Calibri",sans-serif;font-weight:normal'>template grid in single-subject head coordinates, superimposed onto the head model my looks different than the plot of the manual (see below). Could this be related to the fact that the singleshell is not used when preparing the head model? Or might there be something else wrong in my code?</span></strong><strong><span style='font-family:"Calibri",sans-serif'><o:p></o:p></span></strong></span></p><p class=MsoNormal><strong><span lang=EN-US style='font-family:"Calibri",sans-serif'>My plot<o:p></o:p></span></strong></p><p class=MsoNormal><span style='mso-fareast-language:DE'><img width=230 height=174 id="Grafik_x0020_3" src="cid:image006.jpg@01D31AC7.82B12D60"></span><strong><span lang=EN-US style='font-family:"Calibri",sans-serif'><o:p></o:p></span></strong></p><p class=MsoNormal><strong><span lang=EN-US style='font-family:"Calibri",sans-serif'>The plot in the manual<o:p></o:p></span></strong></p><p class=MsoNormal><span style='mso-fareast-language:DE'><img width=300 height=225 id="Grafik_x0020_2" src="cid:image003.png@01D31AC7.7EBE4850" alt=fig3></span><strong><span lang=EN-US style='font-family:"Calibri",sans-serif'><o:p></o:p></span></strong></p><p class=MsoNormal><strong><span lang=EN-US style='font-family:"Calibri",sans-serif'><o:p> </o:p></span></strong></p><p class=MsoNormal><strong><span lang=EN-US style='font-family:"Calibri",sans-serif'>The full code is: <o:p></o:p></span></strong></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:forestgreen'>% and this is where the template source models are</span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> templatedir = fullfile(ftdir, </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>'template'</span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>, </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>'sourcemodel'</span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>);</span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> load(fullfile(templatedir, </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>'standard_sourcemodel3d8mm'</span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>));</span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> template = sourcemodel;</span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> clear </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>sourcemodel</span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>;</span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:forestgreen'>% inverse-warp the template grid to subject specific coordinates </span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> cfg = [];</span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> cfg.grid.warpmni = </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>'yes'</span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>;</span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> cfg.grid.template = template; </span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> cfg.grid.nonlinear = </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>'yes'</span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>; </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:forestgreen'>% use non-linear normalization</span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> cfg.mri = mri_spm_rs; </span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> cfg.grid.unit = </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>'mm'</span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>;</span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> sourcemodel = ft_prepare_sourcemodel(cfg);<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>figure; hold </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>on</span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:forestgreen'>% plot all objects in one figure</span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> ft_plot_mesh(sourcemodel.pos(sourcemodel.inside,:)); </span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'> ft_plot_vol(hdm, </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>'facecolor'</span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>, </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>'cortex'</span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>, </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>'edgecolor'</span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>, </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>'none'</span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>);alpha </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>0.4</span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>; camlight;</span><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:12.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Any help is really appreciated<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Myriad Pro",sans-serif;color:gray;mso-fareast-language:DE'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:1.0pt;mso-fareast-language:DE'><o:p> </o:p></span></p><p class=MsoNormal style='line-height:115%'><span style='mso-fareast-language:DE'><img width=280 height=71 id="Bild_x0020_1" src="cid:image007.jpg@01D31AC7.82B12D60" alt=Unbenannt-1></span><b><span style='font-size:10.5pt;line-height:115%;font-family:"Myriad Pro",sans-serif;color:#7F7F7F;mso-fareast-language:DE'><o:p></o:p></span></b></p><p class=MsoNormal style='line-height:115%'><b><span style='font-size:10.5pt;line-height:115%;font-family:"Myriad Pro",sans-serif;color:#7F7F7F;mso-fareast-language:DE'>E-Mail</span></b><span style='font-size:10.5pt;line-height:115%;font-family:"Myriad Pro",sans-serif;color:#7F7F7F;mso-fareast-language:DE'>: </span><span style='mso-fareast-language:DE'><a href="mailto:cornelia.quaedflieg@uni-hamburg.de"><span style='font-size:10.5pt;line-height:115%;font-family:"Myriad Pro",sans-serif;color:#7F7F7F'>cornelia.quaedflieg@uni-hamburg.de</span></a></span><span style='font-size:10.5pt;line-height:115%;font-family:"Myriad Pro",sans-serif;color:#7F7F7F;mso-fareast-language:DE'> <o:p></o:p></span></p><p class=MsoNormal style='line-height:115%'><b><span style='font-size:10.5pt;line-height:115%;font-family:"Myriad Pro",sans-serif;color:#7F7F7F;mso-fareast-language:DE'>Tel.</span></b><span style='font-size:10.5pt;line-height:115%;font-family:"Myriad Pro",sans-serif;color:#7F7F7F;mso-fareast-language:DE'>: </span><span style='mso-fareast-language:DE'><a href="tel:+49%2040%2042838-5448"><span style='font-size:10.5pt;line-height:115%;font-family:"Myriad Pro",sans-serif;color:#7F7F7F'>+49 40 42838-5448</span></a></span><span style='font-size:10.5pt;line-height:115%;font-family:"Myriad Pro",sans-serif;color:#7F7F7F;mso-fareast-language:DE'> <b>Website</b>: </span><span style='mso-fareast-language:DE'><a href="https://www.psy.uni-hamburg.de/arbeitsbereiche/kognitionspsychologie/personen/quaedflieg-conny.html"><span style='font-size:10.5pt;line-height:115%;font-family:"Myriad Pro",sans-serif;color:#66B0FB'>Hyperlink</span></a></span><span style='font-size:10.5pt;line-height:115%;font-family:"Myriad Pro",sans-serif;color:#7F7F7F;mso-fareast-language:DE'><o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>