<div dir="ltr">Hello,<div>I'm Sara Cinelli<br><div>I'm sorry for writing again, but I checked what you told me in the previous email, but everything was already set the right way. </div></div><div>I have the same problem which I am reporting below together with the entire code.</div><div>Thank you again, have a great day.</div><div><br></div><div>Regards,</div><div><br></div><div>Sara</div><div><div class="gmail-rtcContent" style="padding:30px"><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% read and visualize the anatomical data</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">mrifile = <span style="color:rgb(167,9,245)">'./dicom/00000113.dcm'</span>;</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">mri_orig = ft_read_mri(mrifile);</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% We also read the geometrical data from the fif file.</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">dataset = <span style="color:rgb(167,9,245)">'oddball1_mc_downsampled.fif'</span>;</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">grad    = ft_read_sens(dataset, <span style="color:rgb(167,9,245)">'senstype'</span>, <span style="color:rgb(167,9,245)">'meg'</span>);<span style="color:rgb(0,128,19)">% information about the MEG magnetometer and gradiometer positions (the "grad” structure)</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">elec    = ft_read_sens(dataset, <span style="color:rgb(167,9,245)">'senstype'</span>, <span style="color:rgb(167,9,245)">'eeg'</span>); <span style="color:rgb(0,128,19)">% about the EEG electrodes (the "elec" structure)</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">shape   = ft_read_headshape(dataset, <span style="color:rgb(167,9,245)">'unit'</span>, <span style="color:rgb(167,9,245)">'cm'</span>); <span style="color:rgb(0,128,19)">% information about the head shape</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% </span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% figure</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% ft_plot_headshape(shape);</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% %ft_plot_sens(grad, 'style', '*b');</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% ft_plot_sens(elec, 'style', '*g');</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% view([1 0 0])</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% print -dpng natmeg_dip_geometry1.png</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">%visualize the anatomical MRI </span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">figure</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg = [];</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">ft_sourceplot(cfg, mri_orig);</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">save <span style="color:rgb(167,9,245)">mri_orig mri_orig</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">%% Coregistration the anatomical MRI to MEG coordinate system</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg = [];</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg.method = <span style="color:rgb(167,9,245)">'interactive'</span>;</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg.coordsys = <span style="color:rgb(167,9,245)">'neuromag'</span>;</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">[mri_realigned1] = ft_volumerealign(cfg, mri_orig);</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">save <span style="color:rgb(167,9,245)">mri_realigned1 mri_realigned1</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% </span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg = [];</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg.method = <span style="color:rgb(167,9,245)">'headshape'</span>;</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg.headshape = shape;</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">[mri_realigned2] = ft_volumerealign(cfg, mri_realigned1);</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg = [];</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg.resolution = 1;</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg.xrange = [-100 100];</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg.yrange = [-110 140];</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg.zrange = [-80 120];</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">mri_resliced = ft_volumereslice(cfg, mri_realigned2);</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">save <span style="color:rgb(167,9,245)">mri_resliced mri_resliced</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% figure</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% ft_sourceplot([], mri_resliced);</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% print -dpng natmeg_dip_mri_resliced.png</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% the low-level plotting functions do not know how to deal with units,</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% so make sure we have the MRI expressed in cm as well</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">mri_resliced_cm = ft_convert_units(mri_resliced, <span style="color:rgb(167,9,245)">'cm'</span>);</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">save <span style="color:rgb(167,9,245)">mri_resliced_cm mri_resliced_cm</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">%% Construct the MEG volume conduction model</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% segmentazione</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg           = [];</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">cfg.output    = {<span style="color:rgb(167,9,245)">'brain'</span>, <span style="color:rgb(167,9,245)">'skull'</span>, <span style="color:rgb(167,9,245)">'scalp'</span>};</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">mri_segmented = ft_volumesegment(cfg, mri_resliced); </span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(0,128,19)">% copy the anatomy into the segmented mri</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">mri_segmented.anatomy = mri_resliced.anatomy;</span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre">save <span style="color:rgb(167,9,245)">mri_segmented mri_segmented</span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(167,9,245)"><br></span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><span style="color:rgb(167,9,245)"><br></span></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><font color="#000000">The error I have is the following:</font></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace"><span style="white-space:pre"><font color="#000000"><br></font></span></div><div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace">Error using ft_affinecoordinates<br>converting from scanras to acpc is not supported<br><br>Error in ft_convert_coordsys (line 169)<br>  initial = ft_affinecoordinates(object.coordsys, target);<br><br>Error in ft_volumesegment (line 301)<br>    mri = ft_convert_coordsys(mri, 'acpc');<br></div></div></div></div>