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Hi Tibor,
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<div class="">Let me deliberately ignore your follow up questions for now, and focus on the grand scheme of things, and ask a question back: </div>
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<div class="">using the simbio headmodel, and the (it seems) cortically constrained source model as an input to ft_prepare_leadfield, does this result in dipoles which are inconsistently classified as ‘inside’, (as having a ’true’ for the corresponding entry
in the inside-field) while the corresponding entry in the lead field cell-array is empty?</div>
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<div class="">If so, this needs to be fixed, because it is incorrect behavior of the fieldtrip code. Again, looking forward to a PR that fixes this (possible) issue.</div>
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<div class="">Best wishes,</div>
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<div class="">Jan-Mathijs</div>
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<div class="">On 20 Oct 2020, at 11:44, <a href="mailto:tibor.auer@gmail.com" class="">
tibor.auer@gmail.com</a> wrote:</div>
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<span class="">Dear Diego and Jan-Mathijs,<o:p class=""></o:p></span></div>
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<span class="">Thank you for your valuable input.<o:p class=""></o:p></span></div>
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<span class="">I am using simbio headmodel with 5 tissue compartments.<o:p class=""></o:p></span></div>
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<span class="">I have looked into the code and data, and<span class="Apple-converted-space"> </span></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 class=""></o:p></div>
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<span class="">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 class=""></o:p></span></div>
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<span class="">I understand that the locations I am showing on the attached figure are not of interest anyway.<o:p class=""></o:p></span></div>
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<span class=""><o:p class=""> </o:p></span></div>
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Kind regards,<o:p class=""></o:p></div>
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Tibor<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<b class=""><span style="color: rgb(34, 42, 53);" class="">Auer, Tibor M.D. Ph.D.<o:p class=""></o:p></span></b></div>
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<a href="mailto:tibor.auer@gmail.com" style="color: blue; text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">tibor.auer@gmail.com</span></a><o:p class=""></o:p></div>
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<span style="color: rgb(34, 42, 53);" class="">+44-7906-863837<o:p class=""></o:p></span></div>
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<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" style="color: blue; text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">@TiborAuer</span></a><o:p class=""></o:p></div>
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<span class=""><o:p class=""> </o:p></span></div>
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<b class="">From:</b><span class="Apple-converted-space"> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" style="color: blue; text-decoration: underline;" class="">fieldtrip-bounces@science.ru.nl</a>><span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>Schoffelen, J.M. (Jan Mathijs)<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>20 October 2020 09:49<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" style="color: blue; text-decoration: underline;" class="">fieldtrip@science.ru.nl</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [FieldTrip] Source reconstruction - low-rank leadfield<o:p class=""></o:p></div>
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Hi Tibor, and Jefe,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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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 class=""></o:p></div>
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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 class=""></o:p></div>
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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 class=""></o:p></div>
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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 class=""></o:p></div>
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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 class=""></o:p></div>
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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 class=""></o:p></div>
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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 class=""></o:p></div>
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I am looking forward for a PR that addresses this.<o:p class=""></o:p></div>
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Best wishes,<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Jan-Mathijs<o:p class=""></o:p></div>
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On 20 Oct 2020, at 10:26, Diego Lozano-Soldevilla <<a href="mailto:dlozanosoldevilla@gmail.com" style="color: blue; text-decoration: underline;" class="">dlozanosoldevilla@gmail.com</a>> wrote:<o:p class=""></o:p></div>
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Dear Tibor and FieldTrippers<o:p class=""></o:p></div>
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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 class=""></o:p></div>
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Yours sincerely,<o:p class=""></o:p></div>
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Diego<o:p class=""></o:p></div>
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On Mon, 19 Oct 2020 at 20:17, <<a href="mailto:tibor.auer@gmail.com" style="color: blue; text-decoration: underline;" class="">tibor.auer@gmail.com</a>> wrote:<o:p class=""></o:p></div>
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Dear FieldTrippers,<o:p class=""></o:p></div>
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<o:p class=""></o:p></div>
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I have some questions regarding source reconstruction.<o:p class=""></o:p></div>
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We use eLORETA, which runs fine for most participants, however, I receive this error message for quite a few:<o:p class=""></o:p></div>
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<i class="">the forward solutions have a different rank for each location, which is not supported</i><o:p class=""></o:p></div>
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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 class=""></o:p></div>
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Kind regards,<o:p class=""></o:p></div>
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Tibor<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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<o:p class=""></o:p></div>
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<b class=""><span style="color: rgb(34, 42, 53);" class="">Auer, Tibor M.D. Ph.D.</span></b><o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span style="color: rgb(0, 102, 255);" class="">Research Fellow</span></b><o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span style="color: rgb(0, 102, 255);" class="">School of Psychology, Faculty of Health and Medical Sciences</span></b><o:p class=""></o:p></div>
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University of Surrey, Guildford GU2 7XH<o:p class=""></o:p></div>
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<a href="mailto:T.Auer@surrey.ac.uk" target="_blank" style="color: blue; text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">T.Auer@surrey.ac.uk</span></a><o:p class=""></o:p></div>
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<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" style="color: blue; text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">@TiborAuer</span></a><o:p class=""></o:p></div>
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mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="color: blue; text-decoration: underline; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://doi.org/10.1371/journal.pcbi.1002202" style="color: blue; text-decoration: underline; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://doi.org/10.1371/journal.pcbi.1002202</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
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