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<p style="font-family: Arial;" class="MsoNormal"><font size="3">Dear Fieldtrip users and developers,</font></p>
<p style="font-family: Arial;" class="MsoNormal"><font size="3"> </font></p>
<p style="font-family: Arial;" class="MsoNormal"><font size="3">I would like to start using Fieldtrip for the source analysis of the MEG data, but<br>
</font></p>
<p style="font-family: Arial;" class="MsoNormal"><font size="3">I have some problem with mri segmentation using Neuromag-306 .fif MRI file.</font></p>
<p style="font-family: Arial;" class="MsoNormal"><font size="3"> </font></p>
<p style="font-family: Arial;" class="MsoNormal"><font size="3">I do:</font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3">1) import .fif, (Coordinate alignment was already done in Neuromag).</font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">mriname =
</span><span style="font-size: 10pt; color: rgb(160, 32, 240);">'NEUROMAGxxx.fif'</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">[mri] = ft_read_mri(mriname)</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">cfg<span style="">
</span>= [];<span style=""> </span></span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">ft_sourceplot(cfg,mri);</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;"><br>
</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3">***** attachment: mri.jpg ******<br>
</font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"> </font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3">2) do segmentation</font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">cfg<span style="">
</span>= [];</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">cfg.template<span style="">
</span>= </span><span style="font-size: 10pt; color: rgb(160, 32, 240);">'T1.nii'</span><span style="font-size: 10pt; color: black;">;
</span><span style="font-size: 10pt; color: forestgreen;">%spm8</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">cfg.coordsys<span style="">
</span>= </span><span style="font-size: 10pt; color: rgb(160, 32, 240);">'neuromag'</span><span style="font-size: 10pt; color: black;">;</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">cfg.write<span style="">
</span>= </span><span style="font-size: 10pt; color: rgb(160, 32, 240);">'no'</span><span style="font-size: 10pt; color: black;">;</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">cfg.name<span style="">
</span>= </span><span style="font-size: 10pt; color: rgb(160, 32, 240);">'temp'</span><span style="font-size: 10pt; color: black;">;</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">cfg.interactive<span style="">
</span>= </span><span style="font-size: 10pt; color: rgb(160, 32, 240);">'yes'</span><span style="font-size: 10pt; color: black;">;</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">[segmentedmri]<span style="">
</span>= ft_volumesegment(cfg, mri)</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;"> </span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">3) plot the original and segmented mri</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">cfg<span style="">
</span>= [];</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">test.dim = [512<span style="">
</span>512 180];</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">test<span style="">
</span>= segmentedmri;</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">test.avg.pow<span style="">
</span>= test.gray+test.white;</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">test.anatomy<span style="">
</span>= mri.anatomy;</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">cfg.funparameter<span style="">
</span>= </span><span style="font-size: 10pt; color: rgb(160, 32, 240);">'avg.pow'</span><span style="font-size: 10pt; color: black;">;</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">cfg.interactive<span style="">
</span>= </span><span style="font-size: 10pt; color: rgb(160, 32, 240);">'yes'</span><span style="font-size: 10pt; color: black;">;</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;">ft_sourceplot(cfg,test);</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;"><br>
</span></font></p>
<font size="3">***** attachment : mri_segmented.jpg ******</font>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;"><br>
</span></font></p>
<p class="MsoNormal" style="font-family: Arial;"><font size="3"><span style="font-size: 10pt; color: black;"><span style=""><br>
</span></span></font></p>
<p style="font-family: Arial;" class="MsoNormal"><font size="3">Apparently, there is a displacement of the segmented mri image. It seems also that the
<span style=""> </span>segmented mri <span style=""> </span>is bigger then the original mri.<span style="">
</span></font></p>
<p style="font-family: Arial;" class="MsoNormal"><font size="3">The similar (although not the same) picture is observed when I do coordinate alignment in the MNE and use the /sets/CORxxx.fif saved from the MNE sohtware.</font></p>
<p style="font-family: Arial;" class="MsoNormal"><font size="3">I have seen some discussions on this topic, but I have not found the solution.
<br>
</font></p>
<p style="font-family: Arial;" class="MsoNormal"><font size="3"><br>
</font></p>
<p style="font-family: Arial;" class="MsoNormal"><font size="3">Should I <span style="font-size: 10pt;"> swap x and y coordinates? How can I do it?</span></font>
<style>@font-face {
font-family: "\FF2D \FF33 \660E \671D ";
}@font-face {
font-family: "Cambria Math";
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<p style="font-family: Arial;" class="MsoNormal"><br>
</p>
<p style="font-family: Arial;" class="MsoNormal"><font size="3">I would be most grateful for help!</font></p>
<p style="font-family: Arial;" class="MsoNormal"><br>
</p>
<p style="font-family: Arial;" class="MsoNormal"><font size="3">Elena<br>
</font></p>
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