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<p class="MsoNormal">Dear fieldTrip Users,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am trying to run a dipole fit with the nonlinear grid search and a beamformer scan on a simulated data set, to compare the results.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">My simulated dipole is at the MNI coordinates [32.8 -85.8 28]. It is shown in red in DIP_1.jpg. The ft_dipolefitting results for the simulated dipole is in green in DIP_1.jpg.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">When I do the lcmv beamformer scan on the same simulated data and plot them I get results as in POW_1.jpg for avg.pow parameter and NAI_1.jpg for avg.nai parameter. Following is the code I use for the above purpose;<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">cfg = [];<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.vol = curry_vol;<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.elec = sens;<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.grid=template_grid;<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 = 'lcmv';<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.lambda='5%';<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.projectnoise='yes';
<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">source = ft_sourceanalysis(cfg, timelock);<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">load
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">standard_mri.mat</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 = ft_volumereslice([], 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"></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:forestgreen">%% Figure POW_1.jpg<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">% Aligning the measure of power increase with the structural MRI of subject</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=[];</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.downsample=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.parameter=</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'avg.pow'</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">source_int=ft_sourceinterpolate(cfg,source,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"></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:forestgreen">% Plot the interpolated data</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:forestgreen"></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=[];</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">'slice'</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.funparameter=</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'avg.pow'</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">figure,ft_sourceplot(cfg,source_int)</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"></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:forestgreen">%% Figure NAI_1.jpg</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:forestgreen">% compute the neural activity index, i.e. projected power divided by</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:forestgreen">% projected noise</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:forestgreen"></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">sourceNAI=source;</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">sourceNAI.avg.nai=source.avg.pow./source.avg.noise;
</span><span style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">%neural activity index calculation</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:forestgreen"></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=[];</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.downsample=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.parameter=</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'avg.nai'</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">sourceNAI_int=ft_sourceinterpolate(cfg,sourceNAI,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"></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"> </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 = [];</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">'slice'</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.funparameter =
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'avg.nai'</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.maskparameter=cfg.funparameter;</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">figure ,ft_sourceplot(cfg, sourceNAI_int);<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="color:black">Can you please direct me to what I am doing wrong or missing in my code to get sensible beamformer scan results. When I read the source_int.avg.pow and sourceNAI_int.avg.nai most of
the values are NaN’s. <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="color:black">Many amny thanks in advance.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="color:black">Regards<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="color:black">Imali</span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-AU">Imali Thanuja Hettiarachchi<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-AU">PhD Candidate<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-AU">Centre for Intelligent Systems research<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-AU">Deakin University,
</span><span style="font-size:10.0pt;font-family:"Times New Roman","serif";color:black;mso-fareast-language:EN-AU">Geelong 3217, Australia.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Times New Roman","serif";color:black;mso-fareast-language:EN-AU">Email:
<a href="mailto:ith@deakin.edu.au"><span style="color:blue">ith@deakin.edu.au</span></a><br>
</span><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-AU"><a href="http://www.deakin.edu.au/cisr"><span style="color:blue">www.deakin.edu.au/cisr</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif";mso-fareast-language:EN-AU"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black;mso-fareast-language:EN-AU"><img border="0" width="70" height="73" id="Picture_x0020_1" src="cid:image001.jpg@01CD5EB9.14274110" alt="Description: Description: Description: cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD@deakin.edu.au"></span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black;mso-fareast-language:EN-AU"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black;mso-fareast-language:EN-AU"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black;mso-fareast-language:EN-AU"><br>
<br>
</span><span style="mso-fareast-language:EN-AU"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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