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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link="#0563C1" vlink="#954F72"><div class=WordSection1><p class=MsoNormal>Dear FT experts,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I am not able to realign a T1 scan using the fiducial points and headshapes of a 4D/BTI system, can anyone help me on this? The “interactive” realignment helped a lot, but the end result was not perfect!<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Here’s what I have tried,:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>individual_mri = ft_read_mri(mripath); % ..\MEG_4D\C-101_T1.nii</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>ft_sourceplot([], individual_mri);<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:12.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal style='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='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.method = </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'flip'</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='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>mri.coordsys = </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'4d'</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='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>individual_mri = ft_volumereslice(cfg, individual_mri);</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>ft_sourceplot([], individual_mri);</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>individual_mri = ft_convert_units(individual_mri, </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'m'</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><o:p> </o:p></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>headshape = ft_read_headshape(headpath); % ..\MEG_4D\hs_file</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>mri_fids = headshape.fid.pos;<o:p></o:p></span></p><p class=MsoNormal style='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='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='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.fiducial.nas = mri_fids(1,:);</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.fiducial.lpa = mri_fids(2,:);</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.fiducial.rpa = mri_fids(3,:);</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='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'>'4d'</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='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.method = </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'fiducial'</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='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>mri_realigned = ft_volumerealign(cfg, individual_mri);</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='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='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'>'4d'</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='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.headshape = headshape;</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>cfg.method = </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'headshape'</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='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>mri_realigned = ft_volumerealign(cfg, individual_mri);<o:p></o:p></span></p><p class=MsoNormal style='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='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:forestgreen'>% check that the MRI is consistent after realignment</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>ft_determine_coordsys(mri_realigned, </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>'interactive'</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'>'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='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>hold </span><span style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'>on</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:forestgreen'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>drawnow; </span><span style='font-size:10.0pt;font-family:"Courier New";color:forestgreen'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>ft_plot_headshape(headshape);</span><span style='font-size:12.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:12.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal>Data can be found at,<o:p></o:p></p><p class=MsoNormal>https://www.dropbox.com/sh/e74pt2uc08q6z4q/AAB3fkp_9gvJxi-YtO0muRSca?dl=0<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Best, <o:p></o:p></p><p class=MsoNormal>Vahab<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>