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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thank you for these thoughtful comments. I agree with you Sarang that the noise level is as important as the idea of longer-reaching magnetometers. Some sanity
checks on the magnetometers reveals much more freq specific noise, but I don’t know where to draw the line for trade-off between noise and the choice of channels.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I might try the different suggestions from you, Jan-Mathijs, and if I do, I will let you know about the results.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">An interesting read otherwise could be your own paper Sarang: Characterizing hippocampal dynamics with MEG: A systematic<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">review and evidence-based guidelines.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">It seems in this that gradiometers are just fine to localise deeper sources such as hippocampus.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Casper
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> fieldtrip [mailto:fieldtrip-bounces@science.ru.nl]
<b>On Behalf Of </b>sarang@cfin.au.dk<br>
<b>Sent:</b> 15 November 2019 10:52<br>
<b>To:</b> fieldtrip@science.ru.nl<br>
<b>Subject:</b> Re: [FieldTrip] Magnetometers and gradiometers for source localisation<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Casper and Jan Mathijs,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Oops, I missed Jan Mathijs' reply and now see that there's been quite a bit more progress on this, so hopefully it'll be less DIY going forward. :-) Looking forward to try out these functions and the upcoming documentation/presentations.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Cheers<o:p></o:p></p>
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<p class="MsoNormal">Sarang<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Fri, 2019-11-15 at 09:39 +0000, Schoffelen, J.M. (Jan Mathijs) wrote:<o:p></o:p></p>
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<p class="MsoNormal">Hi Casper, <o:p></o:p></p>
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<p class="MsoNormal">These are all very good and relevant questions. As a matter of fact, a group of colleagues and friends (i.e. methods people, epilepsy researchers and core developers of fieldtrip/mne_python/spm/brainstorm)) have been working on this topic
on and off over the past years, meeting at Aston University, to try and understand the best way to do beamforming analysis on Elekta MEG data. We think that we now understand what’s the best way to approach this, and work is underway to disseminate this to
the community.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">In principle, gradiometers and magnetometers can be combined in a single analysis, but this is unlikely to be optimal. Reason: the different order of magnitude of the signals (which may be aggravated when changing the metric units of the
data (e.g. going from T/m to T/cm for the gradiometers)) causes the covariance matrix (used for the beamformer spatial filter computation) to be differently weighing in the mags versus the grads. Indeed, if it’s deep sources you’re after, you may want to exploit
the depth sensitivity pattern of the mags.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Some software packages address this by differently weighing the sensor types (by means of a baked-in default weighing scheme). A more principled way of addressing this would be to spatially whiten the data (and apply the same whitening
to the leadfields). In FieldTrip this prewhitening can be done with ft_denoise_prewhiten, using the covariance estimated in a baseline window as the prewhitener. If the balanced gradiometer array is subsequently used for the forward computation, the same prewhitener
is applied to the leadfield, so everything stays consistent.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">One thing that is important to take into account, is the rank-deficiency of maxfiltered data. This can cause problems in the mathematical inversion of the covariance matrix, when done inappropriately. In order to have more flexibility in
optimally inverting covariance matrices, we now have a dedicated ft_inv function (in fieldtrip/private), which allows for different ways of (regularized) matrix inversions. For maxfiltered filtered data, it would be recommended to use a ‘kappa’ parameter for
inversion, i.e. to truncate the svd of the coviance matrix at (or just below) its rank.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Currently I am working on some documentation (that uses the Wakeman and Henson dataset) that demonstrates some of these issues. It will be presented at this years practicalMEEG workshop in Paris (<a href="http://practicalmeeg2019.org">http://practicalmeeg2019.org</a>),
so stay tuned! This documentation will become available soon.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best wishes,<o:p></o:p></p>
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<p class="MsoNormal">Jan-Mathijs<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On 15 Nov 2019, at 10:18, Casper Kerren <<a href="mailto:C.Kerren@pgr.bham.ac.uk">C.Kerren@pgr.bham.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Hi,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I am currently source localising an effect using LCMV on Elekta MEG data. I have both gradiometers and magnetometers and have until recently treated these as the same when
preparing the leadfield. However, after having had discussions with my colleagues about the different units and strength for grads and mags, we are hesitant as to what might be the best way of selecting channels. I have searched the fiedltrip mailing list,
and have found some answers, but nothing that I can say is very convincing. Could someone point me in the right direction regarding this? Perhaps someone who has done some checks on using both grads and mags and using only grads or mags. We are interested
in a deeper source, and naively thought that magnetometers would be necessary to include. However, is this just as I say: naïve?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">In the ft_prepareleadfield function I can see that gradiometers is the only channels that are thought of being included, so does fieldtrip actually expect us to exclude magnetometers?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Kind regards,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Casper Kerrén, PhD student</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">School of Psychology <br>
College of Life and Environmental Sciences <br>
University of Birmingham <br>
Edgbaston <br>
Birmingham B15 2TT<br>
e-mail: <a href="mailto:cxk699@student.bham.ac.uk"><span style="color:purple">cxk699@student.bham.ac.uk</span></a> <br>
<br>
<br>
</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Helvetica","sans-serif"">_______________________________________________<br>
fieldtrip mailing list<br>
</span><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip"><span style="font-size:10.5pt;font-family:"Helvetica","sans-serif";color:purple">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</span></a><span style="font-size:10.5pt;font-family:"Helvetica","sans-serif""><br>
</span><a href="https://doi.org/10.1371/journal.pcbi.1002202"><span style="font-size:10.5pt;font-family:"Helvetica","sans-serif";color:purple">https://doi.org/10.1371/journal.pcbi.1002202</span></a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<pre>_______________________________________________<o:p></o:p></pre>
<pre>fieldtrip mailing list<o:p></o:p></pre>
<p class="MsoNormal"><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip"><o:p></o:p></a></p>
<pre><u><span style="color:blue"><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<span style="color:windowtext;text-decoration:none"><o:p></o:p></span></a></span></u></pre>
<p class="MsoNormal"><o:p> </o:p></p>
<pre><o:p> </o:p></pre>
<p class="MsoNormal"><a href="https://doi.org/10.1371/journal.pcbi.1002202"><o:p></o:p></a></p>
<pre><u><span style="color:blue"><a href="https://doi.org/10.1371/journal.pcbi.1002202">https://doi.org/10.1371/journal.pcbi.1002202<span style="color:windowtext;text-decoration:none"><o:p></o:p></span></a></span></u></pre>
<p class="MsoNormal"><o:p> </o:p></p>
<pre><o:p> </o:p></pre>
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