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Hi Sara,
<div class=""><br class="">
</div>
<div class="">The fact that the error still mentions: "<span style="font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">converting from scanras to acpc is not supported</span><font face="Menlo, Monaco, Consolas, Courier New, monospace" size="2" class="">” </font>means
that you did something not quite right.</div>
<div class=""><br class="">
</div>
<div class="">The step that calls ft_volumerealign for the first time, i.e. using mri_orig as an input, and producing mri_realigned1 should return a structure (i.e. mri_realigned1) with a coordsys-field that is named ’neuromag’.</div>
<div class="">You seem to call ft_volumesegment with an anatomical volume that still has the underspecified (and unsupported) ’scanras’ as coordsys.</div>
<div class=""><br class="">
</div>
<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
</div>
<div class=""><font face="Menlo, Monaco, Consolas, Courier New, monospace" size="2" class=""><br class="">
</font>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 15 Apr 2024, at 11:44, Sara Cinelli via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hello,
<div class="">I'm Sara Cinelli<br class="">
<div class="">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 class="">I have the same problem which I am reporting below together with the entire code.</div>
<div class="">Thank you again, have a great day.</div>
<div class=""><br class="">
</div>
<div class="">Regards,</div>
<div class=""><br class="">
</div>
<div class="">Sara</div>
<div class="">
<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" class=""><span style="color:rgb(0,128,19)" class="">% 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" class="">mrifile = <span style="color:rgb(167,9,245)" class="">
'./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" class="">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" class=""><span style="color:rgb(0,128,19)" class="">% 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" class="">dataset = <span style="color:rgb(167,9,245)" class="">
'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" class="">grad = ft_read_sens(dataset, <span style="color:rgb(167,9,245)" class="">
'senstype'</span>, <span style="color:rgb(167,9,245)" class="">'meg'</span>);<span style="color:rgb(0,128,19)" class="">% 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" class="">elec = ft_read_sens(dataset, <span style="color:rgb(167,9,245)" class="">
'senstype'</span>, <span style="color:rgb(167,9,245)" class="">'eeg'</span>); <span style="color:rgb(0,128,19)" class="">
% 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" class="">shape = ft_read_headshape(dataset, <span style="color:rgb(167,9,245)" class="">
'unit'</span>, <span style="color:rgb(167,9,245)" class="">'cm'</span>); <span style="color:rgb(0,128,19)" class="">
% 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" class=""><span style="color:rgb(0,128,19)" class="">%
</span></span></div>
<div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace">
<span style="white-space:pre" class=""><span style="color:rgb(0,128,19)" class="">% 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" class=""><span style="color:rgb(0,128,19)" class="">% 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" class=""><span style="color:rgb(0,128,19)" class="">% %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" class=""><span style="color:rgb(0,128,19)" class="">% 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" class=""><span style="color:rgb(0,128,19)" class="">% 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" class=""><span style="color:rgb(0,128,19)" class="">% 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" class=""><span style="color:rgb(0,128,19)" class="">%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" class="">figure</span></div>
<div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace">
<span style="white-space:pre" class="">cfg = [];</span></div>
<div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace">
<span style="white-space:pre" class="">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" class="">save <span style="color:rgb(167,9,245)" class="">
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" class=""><span style="color:rgb(0,128,19)" class="">%% 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" class="">cfg = [];</span></div>
<div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace">
<span style="white-space:pre" class="">cfg.method = <span style="color:rgb(167,9,245)" class="">
'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" class="">cfg.coordsys = <span style="color:rgb(167,9,245)" class="">
'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" class="">[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" class="">save <span style="color:rgb(167,9,245)" class="">
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" class=""><span style="color:rgb(0,128,19)" class="">%
</span></span></div>
<div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace">
<span style="white-space:pre" class="">cfg = [];</span></div>
<div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace">
<span style="white-space:pre" class="">cfg.method = <span style="color:rgb(167,9,245)" class="">
'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" class="">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" class="">[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" class="">cfg = [];</span></div>
<div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace">
<span style="white-space:pre" class="">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" class="">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" class="">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" class="">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" class="">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" class="">save <span style="color:rgb(167,9,245)" class="">
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" class=""><span style="color:rgb(0,128,19)" class="">% 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" class=""><span style="color:rgb(0,128,19)" class="">% 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" class=""><span style="color:rgb(0,128,19)" class="">% 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" class=""><span style="color:rgb(0,128,19)" class="">% 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" class=""><span style="color:rgb(0,128,19)" class="">% 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" class="">mri_resliced_cm = ft_convert_units(mri_resliced,
<span style="color:rgb(167,9,245)" class="">'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" class="">save <span style="color:rgb(167,9,245)" class="">
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" class=""><span style="color:rgb(0,128,19)" class="">%% 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" class=""><span style="color:rgb(0,128,19)" class="">% 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" class="">cfg = [];</span></div>
<div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace">
<span style="white-space:pre" class="">cfg.output = {<span style="color:rgb(167,9,245)" class="">'brain'</span>,
<span style="color:rgb(167,9,245)" class="">'skull'</span>, <span style="color:rgb(167,9,245)" class="">
'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" class="">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" class=""><span style="color:rgb(0,128,19)" class="">% 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" class="">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" class="">save <span style="color:rgb(167,9,245)" class="">
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" class=""><span style="color:rgb(167,9,245)" class=""><br class="">
</span></span></div>
<div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace">
<span style="white-space:pre" class=""><span style="color:rgb(167,9,245)" class=""><br class="">
</span></span></div>
<div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace">
<span style="white-space:pre" class=""><font class="">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" class=""><font class=""><br class="">
</font></span></div>
<div class="gmail-lineNode" style="font-size:10pt;font-family:Menlo,Monaco,Consolas,"Courier New",monospace">
Error using ft_affinecoordinates<br class="">
converting from scanras to acpc is not supported<br class="">
<br class="">
Error in ft_convert_coordsys (line 169)<br class="">
initial = ft_affinecoordinates(object.coordsys, target);<br class="">
<br class="">
Error in ft_volumesegment (line 301)<br class="">
mri = ft_convert_coordsys(mri, 'acpc');<br class="">
</div>
</div>
</div>
</div>
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https://doi.org/10.1371/journal.pcbi.1002202<br class="">
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