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<p>Dear Lyam,</p>
<p><br>
</p>
<p>the reason why you see a difference between MNE(cond1) -
MNE(cond2) and MNE(cond1 - cond2) is because of the dipole
orientations. The source estimate only retains the magnitude of
the dipoles. See here for some more information about what is
going on:</p>
<p><a class="moz-txt-link-freetext" href="https://4006-1301584-gh.circle-artifacts.com/0/home/ubuntu/mne-python/doc/_build/html/auto_tutorials/plot_dipole_orientations.html">https://4006-1301584-gh.circle-artifacts.com/0/home/ubuntu/mne-python/doc/_build/html/auto_tutorials/plot_dipole_orientations.html</a></p>
<p><br>
</p>
<p> When using fixed orientations, there should not be any
difference. When using loose orientations (the default), MNE(cond1
- cond2) is in my opinion the correct way.<br>
</p>
<br>
regards,<br>
Marijn.<br>
<br>
<div class="moz-cite-prefix">On 04/06/2017 06:42 PM, Lyam Bailey
wrote:<br>
</div>
<blockquote
cite="mid:BN6PR03MB2689A24194CE6F6A6D087A65920D0@BN6PR03MB2689.namprd03.prod.outlook.com"
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Dear MNE users,</p>
<p style="font-family: Calibri, Arial, Helvetica, sans-serif,
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I am analysing surface-based source estimates computed from
evoked MEG data. I would like to extract peak amplitude times
from source estimates of the
<b>difference</b> between two experimental conditions (exp.
and control), and as far as I can tell there are two
approaches to this. One is to calculate the difference prior
to computing source estimates (i.e: exp. evoked - control
evoked) and then compute source estimates (.stc) based on the
returned array. Another is to generate source estimates for
each condition, and then subtract the returned stc files
(exp.stc - control.stc) Unfortunately, these two approaches
yield slightly different results (I suspect this
is due to noise generated by the .stc subtraction) - so which
would be most prudent? Alternatively, is there a different
(more robust) approach that I could use?</p>
<p style="font-family: Calibri, Arial, Helvetica, sans-serif,
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Thanks in advance for any help!</p>
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<br>
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Regards,</p>
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Lyam</p>
<br>
<p><br>
</p>
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<p><span style="color:rgb(0,0,0);
font-family:arial,sans-serif; font-size:12.8px">---------------------------------------------------------</span></p>
<span style="color:rgb(0,0,0)"></span>
<p><span style="color:rgb(0,0,0);
font-family:arial,sans-serif; font-size:12.8px">Lyam
Bailey, BSc.</span><br>
<span style="color:rgb(0,0,0)"></span></p>
<span style="color:rgb(0,0,0)"></span>
<span style="color:rgb(0,0,0)"></span>
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<span style="color:rgb(0,0,0)">Graduate Student</span></div>
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<div style="color:rgb(136,136,136);
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<span style="color:rgb(0,0,0)">Department of Psychology
& Neuroscience</span></div>
<span style="color:rgb(0,0,0)"></span>
<div style="color:rgb(136,136,136);
font-family:arial,sans-serif; font-size:12.8px">
<span style="color:rgb(0,0,0)">Dalhousie University</span></div>
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