<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
span.EmailStyle20
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-GB" link="blue" vlink="purple" style="word-wrap:break-word">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif;" dir="ltr">
<p>Hi Tibor,</p>
<p><br>
</p>
<p>When using a high-detail volume conductor model and cortical source space prior, the source space should be constrained within the gray matter compartment of the model. </p>
<p><br>
</p>
<p>Not knowing in detail the pipelines you used, could it be that you volume conductor model and the source model (cortical sheet) are done with different tools so that part of the cortical sheet model is outside the gray matter compartment of the volume conductor
model?</p>
<p><br>
</p>
<p>When using a distributed imaging solution like eLORETA, the question is not really, are some source locations interesting. If an active source region is left out of the model, the corresponding part of the measurement will be reconstructed by sources in
other regions -> the source estimate will be less correct. Also, if some source region is left out of the model, the model has no information on those sources and can thus not try to separate the activity of those sources from the activity of other source
regions. </p>
<p><br>
</p>
<p>Considering concrete tips, I think JM and other FieldTrip gurus would need more concrete input on what tools you used and in which order.</p>
<p><br>
</p>
<p>Cheers,</p>
<p> Matti</p>
<p></p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Lähettäjä:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> käyttäjän tibor.auer@gmail.com <tibor.auer@gmail.com> puolesta<br>
<b>Lähetetty:</b> 20. lokakuuta 2020 12:44:19<br>
<b>Vastaanottaja:</b> 'FieldTrip discussion list'<br>
<b>Aihe:</b> Re: [FieldTrip] Source reconstruction - low-rank leadfield</font>
<div> </div>
</div>
<div>
<div class="WordSection1">
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Dear Diego and Jan-Mathijs,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Thank you for your valuable input.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">I am using simbio headmodel with 5 tissue compartments.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">I have looked into the code and data, and
</span>Jan-Mathijs’ suspicion is correct. I have attached a figure, which shows the location of the 0-ranked leadfield on the sourcemodel, and they are indeed mostly ‘outside normal brain’ (i.e. ventricles and one spot just outside the cortex).<o:p></o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Based on that, I think it is safe to exclude these locations. However, I wonder how these exlcusions might affect the analysis. Does it mean that I will not have an estimate for the affected locations,
or will they be interpolated? If the former, then will these locations automatically excluded during group analysis, or do I have to explicitly exclude them?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">I understand that the locations I am showing on the attached figure are not of interest anyway.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal">Kind regards,<o:p></o:p></p>
<p class="MsoNormal">Tibor <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><span style="color:#222A35">Auer, Tibor M.D. Ph.D.<o:p></o:p></span></b></p>
<p class="MsoNormal"><a href="mailto:tibor.auer@gmail.com"><span style="color:#0563C1">tibor.auer@gmail.com</span></a><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#222A35">+44-7906-863837<o:p></o:p></span></p>
<p class="MsoNormal"><a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FTiborAuer&data=02%7C01%7Ct.auer%40surrey.ac.uk%7C0da68a9196be4a4fd60108d71a70e11e%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637006944417188277&sdata=aoE%2FhNWj%2F%2F3L8fDDz4S0dMuMTlt2p05mgHaDTXddP4w%3D&reserved=0"><span style="color:#0563C1">@TiborAuer</span></a><o:p></o:p></p>
</div>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b>From:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> <b>
On Behalf Of </b>Schoffelen, J.M. (Jan Mathijs)<br>
<b>Sent:</b> 20 October 2020 09:49<br>
<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Subject:</b> Re: [FieldTrip] Source reconstruction - low-rank leadfield<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Tibor, and Jefe, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I guess that the road to a solution starts by looking into the code, and inspecting what line prompts the error (let me give this one away: line 145 in ft_inverse_eloreta).<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Also, it might be useful to consider not only the source model, but also the volume conduction model, and the method that was used for the forward computation. This was not mentioned in your messages, so it is hard to comment on that.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Then, it may make sense to think about what matrix gives a rank of 0. Typically, the only way in which matlab returns a 0, is in the case of an empty matrix.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thus, the suspicion will rise that the eloreta code is trying to operate on dipole positions for which the corresponding leadfield is an empty matrix.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">The latter typically occurs if that dipole position is considered to be an ‘outside’ position in the forward computation step, e.g. when it is ’sticking out’ of the brain compartment boundary of the volume conduction model (but again, given
the lack of details about the specifics of the volume conduction model etc., this is mere speculation, causing me to already type and think about this for longer than is probably necessary (in case the above is not true) ).<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Then, the overall question might boil down to the question: why does the forward computation consider some dipoles to be outside (i.e. not returning a leadfield matrix for those locations), and why does the inverse computation code (at
least for particular method) not take that into account?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Assuming that all my speculations above are valid, a principled solution will lie in ensuring that the eloreta code only considers the dipole positions with a valid lead field matrix. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I am looking forward for a PR that addresses this.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Best wishes,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Jan-Mathijs<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On 20 Oct 2020, at 10:26, Diego Lozano-Soldevilla <<a href="mailto:dlozanosoldevilla@gmail.com">dlozanosoldevilla@gmail.com</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<div>
<p class="MsoNormal">Dear Tibor and FieldTrippers<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">I'm in the same situation. I excluded those positions but now I'm wondering whether this was a good decision. If somebody know what's happening and how to fix this, please drop a line!<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Yours sincerely,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Diego<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On Mon, 19 Oct 2020 at 20:17, <<a href="mailto:tibor.auer@gmail.com">tibor.auer@gmail.com</a>> wrote:<o:p></o:p></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm">
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Dear FieldTrippers,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I have some questions regarding source reconstruction.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">We use eLORETA, which runs fine for most participants, however, I receive this error message for quite a few:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:36.0pt">
<i>the forward solutions have a different rank for each location, which is not supported</i><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">The rank of the leadfdield is reduced at each sourcemodel position to the default 3. However, it sometimes has an even lower rank (often 0) at certain sourcemodel positions, and
I am not sure how to interpret it. We use a cortical sheet based sourcemodel, and I have noticed that only a handful (<<1%) of positions are affected. My educated guess would be to exclude those positions, but I am not sure how it affects the analysis, either.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Kind regards,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Tibor
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="color:#222A35">Auer, Tibor M.D. Ph.D.</span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="color:#0066FF">Research Fellow</span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="color:#0066FF">School of Psychology, Faculty of Health and Medical Sciences</span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">University of Surrey, Guildford GU2 7XH<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="mailto:T.Auer@surrey.ac.uk" target="_blank"><span style="color:#0563C1">T.Auer@surrey.ac.uk</span></a><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FTiborAuer&data=02%7C01%7Ct.auer%40surrey.ac.uk%7Cdb32da458c424eedef2908d7d4bd1421%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637211780868086968&sdata=zrT5%2FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%3D&reserved=0" target="_blank"><span style="color:#0563C1">@TiborAuer</span></a><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal">_______________________________________________<br>
fieldtrip mailing list<br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<a href="https://doi.org/10.1371/journal.pcbi.1002202" target="_blank">https://doi.org/10.1371/journal.pcbi.1002202</a><o:p></o:p></p>
</blockquote>
</div>
</div>
<p class="MsoNormal">_______________________________________________<br>
fieldtrip mailing list<br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<a href="https://doi.org/10.1371/journal.pcbi.1002202">https://doi.org/10.1371/journal.pcbi.1002202</a><o:p></o:p></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</div>
</body>
</html>