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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'>Dear fieldtrip users,<o:p></o:p></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'><o:p> </o:p></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'>I am running the <b>tutorial: “Create MNI-aligned grids in individual head-space” (CASE 1)</b>. When using the template mri provided on the homepage (i.e. Subject01.mri), it seems like the grid, the resulting vol and the anatomy are not aligned. And even worse: besides the misalignment there seems to be a scaling. Note however, that I am using the exact same parameter as specified on the homepage. For a better understanding see page 1 of Alignment.pdf attached to this mail.<o:p></o:p></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'><o:p> </o:p></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'>I found out that things improve when I use the segmentation procedure specified in the <b>tutorial: “Build a geometrical description of the volume conduction model of the head” (CASE 2). </b>See page 2 of Alignment.pdf.<o:p></o:p></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'><o:p> </o:p></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'><o:p> </o:p></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'>In particular, in <b>CASE 1</b> I do: <o:p></o:p></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'><o:p> </o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg = [];</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.downsample = 2;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.coordsys = </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'ctf'</span><span style='font-size:10.0pt;font-family:"Courier New";color:black'>;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>seg_MNItutorial = ft_volumesegment(cfg, mri);</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:forestgreen'><o:p> </o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:forestgreen'>% plotting case 1<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>seg_MNItutorial.transform = mri.transform;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>seg_MNItutorial.anatomy = mri.anatomy;<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>figure</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.funparameter = </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'gray'</span><span style='font-size:10.0pt;font-family:"Courier New";color:black'>;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>ft_sourceplot(cfg,seg_MNItutorial); </span><span style='font-size:10.0pt;font-family:"Courier New";color:forestgreen'>%segmented gray matter on top</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:12.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:12.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'><o:p> </o:p></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'> While, in <b>CASE 2</b> I do: <o:p></o:p></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'><o:p> </o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg = [];</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.write = </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'no'</span><span style='font-size:10.0pt;font-family:"Courier New";color:black'>;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.coordsys = </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'ctf'</span><span style='font-size:10.0pt;font-family:"Courier New";color:black'>;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.output = {</span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'scalp'</span><span style='font-size:10.0pt;font-family:"Courier New";color:black'>,</span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'skull'</span><span style='font-size:10.0pt;font-family:"Courier New";color:black'>,</span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'brain'</span><span style='font-size:10.0pt;font-family:"Courier New";color:black'>};</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>seg_headmodelTutorial = ft_volumesegment(cfg, mri);<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'><o:p> </o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:forestgreen'>% plotting case 2</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>mri_combine = mri;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>mri_combine.seg = seg_headmodelTutorial.scalp + 3*seg_headmodelTutorial.skull + 6*seg_headmodelTutorial.brain;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>mri_combine.mask = (mri_combine.seg)>0;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg = [];</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.interactive = </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'yes'</span><span style='font-size:10.0pt;font-family:"Courier New";color:black'>;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.funparameter = </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'seg'</span><span style='font-size:10.0pt;font-family:"Courier New";color:black'>;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.funcolormap = </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'jet'</span><span style='font-size:10.0pt;font-family:"Courier New";color:black'>;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.funcolorlim = [0 7];</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.opacitylim = [0 1.5];</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.maskparameter = </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'mask'</span><span style='font-size:10.0pt;font-family:"Courier New";color:black'>;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>figure, ft_sourceplot(cfg,mri_combine);</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:12.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none'><span style='font-size:12.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'>I am confused, why CASE 2 works, while CASE 1 does not. Could anyone explain the differences to me? Is doing it like in CASE 2 correct at all?<o:p></o:p></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'><o:p> </o:p></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'>Thanks a lot in advance!<o:p></o:p></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:normal'>Anette<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>