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<div style="direction:ltr"><span style="font-size:10pt">Dear all, </span>
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<div style="color:rgb(0,0,0); font-family:Tahoma; font-size:10pt">After MNE source analysis with the template MRI(Colin27), <span style="font-size:13.3333px">I want to do parcellation with the AAL atlas. So first I checked how well the </span><span style="font-size:13.3333px">template</span><span style="font-size:13.3333px"> </span><span style="font-size:13.3333px">cortical
sheet and AAL atlas fit with the following code: </span></div>
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</span></div>
<div style="color:rgb(0,0,0); font-family:Tahoma; font-size:10pt"><span style="font-size:13.3333px">--------------------------------------------------------------</span></div>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">aal</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline"> =
</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">ft_read_atlas</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">('C:\</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">MyTemp</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">\Toolbox\fieldtrip\</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">fieldtrip_git</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">\template\atlas\</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">aal</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">\ROI_MNI_V4.nii');</span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">mne_sourcemodel</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">=</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">ft_read_headshape</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">('cortex_8196.surf.gii');</span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline"> </span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">cfg</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline"> = [];
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">cfg.interpmethod</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline"> = 'nearest';
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">cfg.parameter</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline"> = 'tissue';
</span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">mne_sourcemodel_with_label</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline"> =
</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">ft_sourceinterpolate</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">(</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">cfg</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">,
</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">aal</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">,
</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">mne_sourcemodel</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">);</span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline"> </span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">disp</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">(</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">mne_sourcemodel_with_label.tissuelabel</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">')</span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline"> </span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">for </span>
<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">i</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">=1:length(</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">mne_sourcemodel_with_label.tissue</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">)</span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline"> if
</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">mne_sourcemodel_with_label.tissue</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">(</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">i</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">)==0;</span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">
</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">mne_sourcemodel_with_label.tissue</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">(</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">i</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">)=200;</span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline"> end;</span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">end;</span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline"> </span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">ft_plot_mesh</span><span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">(mne_sourcemodel_with_label,'vertexcolor',mne_sourcemodel_with_label.tissue,'edgecolor','black')</span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">colorbar</span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline">---------------------------------------------------------</span></p>
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<span style="font-size:12pt; font-family:Calibri; vertical-align:baseline"><br>
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<span style="color:rgb(0,0,0); font-family:Calibri; font-size:12pt; vertical-align:baseline">The result looks like that the </span><span style="color:rgb(0,0,0); font-family:Tahoma; font-size:13.3333px">parcellation</span><span style="color:rgb(0,0,0); font-family:Tahoma; font-size:13.3333px"> of
the </span><font face="Calibri"><span style="font-size:12pt">sulci are not very good. Also parts of the
</span><span style="font-size:16px">cerebellum</span><span style="font-size:12pt"> are included after </span><span style="font-size:16px">interpolation. </span></font></p>
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<span style="color:rgb(0,0,0); font-family:Calibri; font-size:12pt"><br>
</span></p>
<p style="margin-top:0pt; margin-bottom:0pt; margin-left:0in; direction:ltr; unicode-bidi:embed; word-break:normal">
<span style="color:rgb(0,0,0); font-family:Calibri; font-size:12pt">So I want to ask if there are surface-based atlas available (</span><font face="Calibri"><span style="font-size:16px">preferably also based on the Colin27)? </span></font></p>
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</span></font></p>
<p style="margin-top:0pt; margin-bottom:0pt; margin-left:0in; direction:ltr; unicode-bidi:embed; word-break:normal">
<font face="Calibri"><span style="font-size:16px">And also I noticed the freesurfer pipeline creates cortical parcellation </span></font><span style="font-family:Calibri; font-size:16px"> such as the Destrieux atlas, could I somehow utilize this in creating </span><span style="font-family:Calibri; font-size:16px">surface-based
atlas for my MNE source model?</span></p>
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<font face="Calibri"><span style="font-size:16px">Thanks in advance.</span></font></p>
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</span></font></p>
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<font face="Calibri"><span style="font-size:16px">Best,</span></font></p>
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<div style="margin:0px"><font face="Times New Roman,serif" size="3"><span style="font-size:12pt"><font face="Tahoma,sans-serif" size="2"><span style="font-size:10pt">Weiyong Xu</span></font></span></font></div>
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<div style="margin:0px"><font face="Times New Roman,serif" size="3"><span style="font-size:12pt"><font face="Tahoma,sans-serif" size="2"><span style="font-size:10pt"> </span></font></span></font></div>
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<div style="margin:0px"><font face="Times New Roman,serif" size="3"><span style="font-size:12pt"><font face="Tahoma,sans-serif" size="2"><span style="font-size:10pt">Ph.D. student</span></font></span></font></div>
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<div style="margin:0px"><font face="Times New Roman,serif" size="3"><span style="font-size:12pt"><font face="Tahoma,sans-serif" size="2"><span style="font-size:10pt">Department of Psychology</span></font></span></font></div>
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<div style="margin:0px"><font face="Times New Roman,serif" size="3"><span style="font-size:12pt"><font face="Tahoma,sans-serif" size="2"><span style="font-size:10pt">University of Jyväskylä</span></font></span></font></div>
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