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<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:0cm;text-align:justify;line-height:18.0pt">
<span style="font-size:11.5pt;font-family:"Calibri",sans-serif;color:black">Dear FieldTrippers,<o:p></o:p></span></p>
<p style="margin-bottom:6.0pt;text-align:justify;line-height:18.0pt;font-variant-ligatures: normal;font-variant-caps: normal;orphans: 2;widows: 2;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:11.5pt;font-family:"Calibri",sans-serif;color:black">My name is Alba Xifra Porxas and I am working in the Biosignals and Systems Analysis Lab at McGill University. Currently I am analyzing MEG data from a motor-task paradigm from young
and elderly subjects. I am following the tutorial: Source reconstruction of event-related fields using minimum-norm estimate (http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate).<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:6.0pt;margin-left:0cm;text-align:justify;line-height:18.0pt">
<span style="font-size:11.5pt;font-family:"Calibri",sans-serif;color:black">I am having problems reading the downsampled mesh from MNE suite. When I call FT_READ_HEADSHAPE, I receive the following error message:
<o:p></o:p></span></p>
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<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">>> sourcespace = ft_read_headshape('s003-oct-6-src.fif', 'format', 'mne_source');<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Error using fiff_read_tag (line 178)<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Only two and three dimensional matrices are supported at this time<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Error in mne_read_source_spaces/read_source_space/find_tag (line 288)<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> tag = fiff_read_tag(fid,node.dir(p).pos);<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Error in mne_read_source_spaces/read_source_space (line 254)<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> tag2 = find_tag(this,FIFF.FIFF_MNE_SOURCE_SPACE_NEAREST_DIST);<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Error in mne_read_source_spaces (line 111)<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> this = read_source_space(spaces(k));<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Error in ft_read_headshape (line 391)<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> src = mne_read_source_spaces(filename, 1);<o:p></o:p></span></pre>
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<span style="font-size:11.5pt;font-family:"Calibri",sans-serif;color:black">However, I can visualize it correctly in MNE. The command I used to create the source space is: mne_setup_source_space --ico -6.<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:6.0pt;margin-left:0cm;text-align:justify;line-height:18.0pt">
<span style="font-size:11.5pt;font-family:"Calibri",sans-serif;color:black">Since I have the meshes from FreeSurfer, I tried a workaround. I call FT_READ_HEADSHAPE using lh.orig and rh.orig, which works. I successfully coregister the source space with the sensor-space
and compute source reconstruction using minimum-norm estimation. However, when I try to downsample the output of FT_SOURCEANALYSIS calling FT_VOLUMEDOWNSAMPLE before parcellation, I receive the following error:<o:p></o:p></span></p>
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<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Reference to non-existent field 'dim'.<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Error in ft_volumedownsample (line 100)<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">xsel = 1:cfg.downsample:source.dim(1);<o:p></o:p></span></pre>
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<span style="font-size:11.5pt;font-family:"Calibri",sans-serif;color:black">Even if I manually introduce this missing field ‘dim’, it seems the number of vertices is too big:<o:p></o:p></span></p>
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<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">>> source.dim(1) = length(source.pos);source.dim(2) = length(source.pos);source.dim(3) = length(source.pos);<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">>> cfg = [];cfg.downsample = 4;source_down = ft_volumedownsample(cfg,source);<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Error using repmat<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Maximum variable size allowed by the program is exceeded.<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Error in ndgrid (line 73)<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> varargout{i} = repmat(x,s);<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span lang="ES" style="font-size:9.0pt;font-family:Consolas;color:black">Error in pos2transform (line 25)<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span lang="ES" style="font-size:9.0pt;font-family:Consolas;color:black">[X,Y,Z] = ndgrid(x, y, z);<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Error in ft_checkdata>source2volume (line 1286)<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> data.transform = pos2transform(data.pos, data.dim);<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Error in ft_checkdata (line 350)<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> data = source2volume(data);<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">Error in ft_volumedownsample (line 69)<o:p></o:p></span></pre>
<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">source = ft_checkdata(source, 'datatype', 'volume', 'feedback', 'no');<o:p></o:p></span></pre>
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<p style="mso-margin-top-alt:6.0pt;margin-right:0cm;margin-bottom:6.0pt;margin-left:0cm;text-align:justify;line-height:18.0pt">
<span style="font-size:11.5pt;font-family:"Calibri",sans-serif;color:black">The source I use is as follows:<o:p></o:p></span></p>
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<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">>> display(source)<o:p></o:p></span></pre>
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<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black">source = <o:p></o:p></span></pre>
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<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> time: [1x3900 double]<o:p></o:p></span></pre>
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<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> inside: [255462x1 logical]<o:p></o:p></span></pre>
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<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> pos: [255462x3 double]<o:p></o:p></span></pre>
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<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> method: 'average'<o:p></o:p></span></pre>
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<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> avg: [1x1 struct]<o:p></o:p></span></pre>
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<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> cfg: [1x1 struct]<o:p></o:p></span></pre>
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<pre style="text-align:justify;background:#F7F9FA;border:none;padding:0cm"><span style="font-size:9.0pt;font-family:Consolas;color:black"> dim: [255462 255462 255462]<o:p></o:p></span></pre>
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<span style="font-size:11.5pt;font-family:"Calibri",sans-serif;color:black">Therefore, I am back to where I started. I need to read the fif file from MNE suite.<o:p></o:p></span></p>
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<span style="font-size:11.5pt;font-family:"Calibri",sans-serif;color:black">I uploaded my fif file in Dropbox. Here is the link:<span class="apple-converted-space"> <a href="https://www.dropbox.com/sh/uq181l76353hd8q/AACjTu8KI_rGaXlaDMyw-Diba?dl=0">https://www.dropbox.com/sh/uq181l76353hd8q/AACjTu8KI_rGaXlaDMyw-Diba?dl=0</a><o:p></o:p></span></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:0cm;text-align:justify;line-height:18.0pt">
<span style="font-size:11.5pt;font-family:"Calibri",sans-serif;color:black">Could someone tell me if there is something wrong with the file or with my workaround? Any help would be really appreciated. I am using Fieldtrip version 20170118.<o:p></o:p></span></p>
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<span style="font-size:11.5pt;font-family:"Calibri",sans-serif;color:black">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="mso-fareast-language:EN-CA">Alba Xifra Porxas<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;mso-fareast-language:EN-CA">PhD student,
</span><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;mso-fareast-language:EN-CA">Biosignals and Systems Analysis Lab<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;mso-fareast-language:EN-CA">McGill University, Montr</span><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:#222222;background:white;mso-fareast-language:EN-CA">é</span><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;mso-fareast-language:EN-CA">al,
Canada<o:p></o:p></span></p>
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