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<div class="moz-cite-prefix">Hi Ravi,<br>
<br>
Marios (in CC) promised to send you the short Matlab-script that
we use to transform the diffusion tensors <br>
to conductivity tensors using Tuch's effective medium approach. <br>
<br>
For this approach, please check e.g. the subsection<br>
"Calibrated Finite Element Head Model and Forward Solution"<br>
in<br>
<a class="moz-txt-link-freetext" href="https://link.springer.com/article/10.1007/s10548-017-0568-9">https://link.springer.com/article/10.1007/s10548-017-0568-9</a><br>
<br>
BR<br>
Carsten<br>
<br>
Am 05.11.18 um 18:26 schrieb Ravi Mill:<br>
</div>
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<p style="margin-top:0; margin-bottom:0">Hi Carsten and
Johannes</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Many thanks for
responding, and for developing these great tools!</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">I'm in the process of
acquiring a large diffusion MR dataset from which I can
hopefully create an 'averaged' atlas. From your responses I
think I have a sense of how to integrate the conductivity
tensors derived from this atlas with the Fieldtrip FEM
pipeline.</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">But I was wondering
if you had any advice on how to compute these conductivity
tensors in the first place? From the paper that Carsten
sent, It seems like the FDT program within FSL<span> is what
I need to compute diffusion tensors from the raw diffusion
images (steps 1-6 from the FDT user guide <a
href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Processing_pipeline"
class="OWAAutoLink" id="LPlnk529292"
previewremoved="true" moz-do-not-send="true">https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Processing_pipeline</a>)?
Seemingly, these diffusion tensors need to then be
converted to conductivity tensors - any advice on how to
do this (or if you could point me to some example code)
would be greatly appreciated. </span></p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Thanks</p>
<p style="margin-top:0; margin-bottom:0">Ravi</p>
<p style="margin-top:0; margin-bottom:0"><br>
<span></span></p>
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<a
id="LPUrlAnchor_15414382644960.5199188323612385"
href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Processing_pipeline"
target="_blank" style="text-decoration: none;"
moz-do-not-send="true">FDT/UserGuide - FslWiki -
University of Oxford</a></div>
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fsl.fmrib.ox.ac.uk</div>
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hidden;">
Eddy Current Correction. Eddy currents in the
gradient coils induce (approximate) stretches and
shears in the diffusion weighted images. These
distortions are different for different gradient
directions.</div>
</td>
</tr>
</tbody>
</table>
</div>
<br>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span>Thanks again<br>
Ravi</span></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b>
fieldtrip <a class="moz-txt-link-rfc2396E" href="mailto:fieldtrip-bounces@science.ru.nl"><fieldtrip-bounces@science.ru.nl></a> on behalf
of Johannes Vorwerk <a class="moz-txt-link-rfc2396E" href="mailto:j.vorw01@gmail.com"><j.vorw01@gmail.com></a><br>
<b>Sent:</b> Monday, October 29, 2018 10:14:16 AM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] Incorporating White Matter
conductivity anisotropy into FEM simbio</font>
<div> </div>
</div>
<meta content="text/html; charset=utf-8">
<div class="" style="word-wrap:break-word">Dear Ravi,
<div class=""><br class="">
</div>
<div class="">as Carsten already said, calculating FEM with
anisotropic conductivities is not directly supported by the
FieldTrip-SimBio implementation. However, if you are willing
to invest a bit of time it is possible to work around this.</div>
<div class=""><br class="">
</div>
<div class="">The „only“ thing that needs to be changed is the
calculation of the FEM stiffness matrix, which is performed
by the routine „calc_stiffness_matrix_val“ in the function
sb_calc_stiff (usually called from ft_prepare_headmodel).
The problem is that FieldTrip does not support anisotropic
conductivities, so that you would have to call
calc_stiffness_matrix_val directly. You can see the correct
call in sb_calc_stiff. For anisotropic conductivities you
have to replace the input „cond“ by a #elements x 6 matrix
containing your anisotropic conductivities in the format "xx
yy zz xy yz zx“. If you now follow the normal
FieldTrip-SimBio workflow using the resulting stiffness
matrix, you will get results for anisotropic conductivities.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Johannes</div>
<div class=""><br class="">
</div>
<div>
<blockquote type="cite" class="">
<div class="">Am 29.10.2018 um 12:31 schrieb Carsten
Wolters <<a
href="mailto:carsten.wolters@uni-muenster.de"
class="OWAAutoLink" id="LPlnk144193"
previewremoved="true" moz-do-not-send="true">carsten.wolters@uni-muenster.de</a>>:</div>
<br class="x_Apple-interchange-newline">
<div class="">
<div class="x_moz-cite-prefix"
style="font-family:Helvetica; font-size:12px;
font-style:normal; font-weight:normal;
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text-indent:0px; text-transform:none;
white-space:normal; word-spacing:0px;
background-color:rgb(255,255,255)">
Dear Ravi,<br class="">
<br class="">
1) You can use the pure SimBio-code from<span
class="x_Apple-converted-space"> </span><br class="">
<a class="x_moz-txt-link-freetext OWAAutoLink"
href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mrt.uni-jena.de%2Fsimbio%2Findex.php%2FMain_Page&data=02%7C01%7Crdm146%40newark.rutgers.edu%7Cfd39adb746104deddfa808d63da91b81%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636764193863059067&sdata=cFED89%2BXMUfro9URWv5pWzGC5SnzTqEHT%2FmXd%2F2eB8Q%3D&reserved=0"
originalsrc="https://www.mrt.uni-jena.de/simbio/index.php/Main_Page"
shash="E+sEUfVHsMIGw5FOeiht+gCCWfg6jplHhvLsF4T087oniMFBkYRLSgzGVoyuAWFokF6QyNcBGpl5bbTkBMUWixu7iNa8dgcF4fPtq0kxVDz+MGMOwt9cL1U5tI5+eVhH6dyyyNiKGN5PEMI3clCxn72Y8w3E7sw+48UcBXg9pm8="
id="LPlnk649518" previewremoved="true"
moz-do-not-send="true">https://www.mrt.uni-jena.de/simbio/index.php/Main_Page</a><br
class="">
to treat WM anisotropy.<br class="">
While it would in principle also be possible to use
anisotropic conductivities with FieldTrip-SimBio,<span
class="x_Apple-converted-space"> </span><br class="">
this is currently not implemented using
ft_prepare_headmodel. Johannes (in CC), who
implemented<span class="x_Apple-converted-space"> </span><br
class="">
Fieldtrip-SimBio, answered a same question by Junjie
Wu in March 2018:<span class="x_Apple-converted-space"> </span><br
class="">
"Depending on your matlab skills and your available
time, I could help you to give it a<span
class="x_Apple-converted-space"> </span><br class="">
try though. It should be possible with using some
direct function calls instead of the high-level
fieldtrip-functions."<br class="">
<br class="">
2) We recommend<span class="x_Apple-converted-space"> </span><br
class="">
<a class="x_moz-txt-link-freetext OWAAutoLink"
href="https://na01.safelinks.protection.outlook.com/?url=http:%2F%2Fwww.sci.utah.edu%2F~wolters%2FPaperWolters%2F2012%2FRuthottoEtAl_PhysMedBiol_2012.pdf&data=02%7C01%7Crdm146%40newark.rutgers.edu%7Cfd39adb746104deddfa808d63da91b81%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636764193863069076&sdata=tYM5Oabmkx3Gr4R0I1Wqauly3lVENtp1H%2Fnebvcl0pw%3D&reserved=0"
originalsrc="http://www.sci.utah.edu/~wolters/PaperWolters/2012/RuthottoEtAl_PhysMedBiol_2012.pdf"
shash="Sz3Mz6rgQT4j0kJTNIrh1qvaGkhKz2IJJ+KHg4VYldhiXQ7fM+z6RsAzmMwOpKEVD//huxhUqNmOE3OYdzq+SDHvQMAQYUG0VxVbdxRqkdkww+DvYrrmdXf/IzqQSuYyA29cYI4hs6QtJXugo1JDXpodq7CCmQzeA/dAcocsXK8="
id="LPlnk912676" previewremoved="true"
moz-do-not-send="true">http://www.sci.utah.edu/~wolters/PaperWolters/2012/RuthottoEtAl_PhysMedBiol_2012.pdf</a><br
class="">
on individual data. I could imagine that an atlas does
a reasonable job w.r.t. the main<br class="">
bigger fiber tracts such as corpus callosum or
pyramidal tracts, but that the finer details<br
class="">
in the cortices are individual. We always measure T1,
T2 and DTI from each subject<br class="">
and I personally do not have experience with such a
group-level anisotropy compared<span
class="x_Apple-converted-space"> </span><br class="">
to the individual one. Might be interesting to hear
from others what they think!?<br class="">
<br class="">
BR<br class="">
Carsten<br class="">
<br class="">
<br class="">
<br class="">
Am 25.10.18 um 23:05 schrieb Ravi Mill:<br class="">
</div>
<blockquote type="cite" class=""
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style="font-family: Helvetica, Helvetica, EmojiFont,
"Apple Color Emoji", "Segoe UI
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<div class="" style="margin-top:0px;
margin-bottom:0px">Dear Fieldtrippers</div>
<div class="" style="margin-top:0px;
margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px;
margin-bottom:0px">I have applied the FEM simbio
head modeling pipeline implemented in Fieldtrip to
my EEG data. <span class="">My understanding is
that this pipeline assumes isotropic
conductivities for 5 head compartments (as
specified by cfg.conductivity in
ft_prepare_headmodel). </span>After reading some
papers (e.g. Vorwerk et al 2014 <a
href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1016%2Fj.neuroimage.2014.06.040&data=02%7C01%7Crdm146%40newark.rutgers.edu%7Cfd39adb746104deddfa808d63da91b81%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636764193863069076&sdata=GbsiChTzmUZMEBsH1k44etRdVJUcUQ6SskLJtnzkbSk%3D&reserved=0"
originalsrc="https://doi.org/10.1016/j.neuroimage.2014.06.040"
shash="ErJITSbdBRFdy7X7vIrKDZMlbdKbOko45+mw+79EFXIc61LCdXwAYEmfPba55QzS1C4V0mf0ZiyJZqO3Khf8+KTgp3xaHd5/13wt9mp4gG14rftp8Pi4E7TndLevMu5608yiRFyLV4sceJtVKvtJS6soMOCKEflB/2KOkSmS94o="
class="x_OWAAutoLink" id="LPlnk216235"
previewremoved="true" moz-do-not-send="true">https://doi.org/10.1016/j.neuroimage.2014.06.040</a>),
it seems like incorporating white matter
conductivity anisotropy has a relatively small
albeit significant effect on the source solution.
I am interested in comparing FEM results when
treating white matter as anisotropic. <span
class="" style="font-size:12pt">My questions are
as follows:</span></div>
<div class="" style="margin-top:0px;
margin-bottom:0px"><span class=""
style="font-size:12pt"><br class="">
</span></div>
<ol class="" style="margin-bottom:0px;
margin-top:0px">
<li class="">Is there a way to implement the FEM
simbio head model whilst treating WM as
anisotropic within Fieldtrip? If so, how would
one do this (or are there any resources
available that demonstrate this)?</li>
<li class="">From previous papers and some simbio
documentation (<a
href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mrt.uni-jena.de%2Fsimbio%2Findex.php%2FSIMBIO%2FReleasenotes%2FExamples&data=02%7C01%7Crdm146%40newark.rutgers.edu%7Cfd39adb746104deddfa808d63da91b81%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636764193863079077&sdata=LLPhLC8V85SmMAJbnV%2F15%2Bcs366ek6FQbx81p25mwqA%3D&reserved=0"
originalsrc="https://www.mrt.uni-jena.de/simbio/index.php/SIMBIO/Releasenotes/Examples"
shash="OUH/nWbFzKSSyhH1mGYHm/Ks7+HhHc0oJYAba6xnYl/D0Lz+0SoPitoZ6qnSF84rCNelMyF4xr5GFhCns8QWMkgFj+nfTdGyYBLlo/tt4bJ5UreViLwKIjH9KDa6xhhb9JApZJurR40AEpox0ydsYvSba3GJQ9nBXe/lMQvtq/c="
class="x_OWAAutoLink" id="LPlnk493580"
previewremoved="true" moz-do-not-send="true">https://www.mrt.uni-jena.de/simbio/index.php/SIMBIO/Releasenotes/Examples</a>)
it seems like diffusion MRI data is required to
calculate the WM conductivity for each
individual subject. I only have T1 and T2 scans
for my subjects. So would it be possible to use
WM anisotropic information obtained from some
kind of diffusion MRI group average/atlas
instead (accepting some loss in
subject-level precision)? If so, does such a
group average/atlas exist?</li>
</ol>
<br class="">
<div class="" style="margin-top:0px;
margin-bottom:0px">Any help would be greatly
appreciated!</div>
<div class="" style="margin-top:0px;
margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px;
margin-bottom:0px">Thanks</div>
<div class="" style="margin-top:0px;
margin-bottom:0px">Ravi</div>
<br class="">
<p class="" style="margin-top:0px;
margin-bottom:0px"><span class=""
style="font-size:12pt"></span></p>
<div class=""> </div>
</div>
<br class="">
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<pre class="x_moz-quote-pre">_______________________________________________
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</pre>
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<br class="" style="font-family:Helvetica;
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<pre class="x_moz-signature" cols="72" style="font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; word-spacing:0px; background-color:rgb(255,255,255)">--
Prof. Dr.rer.nat. Carsten H. Wolters
University of Münster
Institute for Biomagnetism and Biosignalanalysis
Malmedyweg 15
48149 Münster, Germany
Phone:
+49 (0)251 83 56904
+49 (0)251 83 56865 (secr.)
Fax:
+49 (0)251 83 56874
Email: <a class="x_moz-txt-link-abbreviated OWAAutoLink" href="mailto:carsten.wolters@uni-muenster.de" id="LPlnk155336" previewremoved="true" moz-do-not-send="true">carsten.wolters@uni-muenster.de</a>
Web: <a class="x_moz-txt-link-freetext OWAAutoLink" href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcampus.uni-muenster.de%2Fbiomag%2Fdas-institut%2Fmitarbeiter%2Fcarsten-wolters%2F&data=02%7C01%7Crdm146%40newark.rutgers.edu%7Cfd39adb746104deddfa808d63da91b81%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636764193863099102&sdata=Xuoiy%2FV4Vfti4QM2bSxaitn%2FxnJeG3vG8UaWnd5XMXI%3D&reserved=0" originalsrc="https://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/carsten-wolters/" shash="samsgyE4Lcw534qdXSIyR66O0j1LTlrvMHX+/IXV+hpERgCM4YC9XoXhviN0V4zejBqo2kWXYrQOh8O/eMH+eDP+FAuHfMrvI+vvrLiUk081U2oRhimpLiF+zmi8muptZQmo13R1Jc0C41vUTtSBM17dYq6V4hXGHJgZ2I3mSpA=" id="LPlnk782212" previewremoved="true" moz-do-not-send="true">https://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/carsten-wolters/</a></pre>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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</pre>
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Prof. Dr.rer.nat. Carsten H. Wolters
University of Münster
Institute for Biomagnetism and Biosignalanalysis
Malmedyweg 15
48149 Münster, Germany
Phone:
+49 (0)251 83 56904
+49 (0)251 83 56865 (secr.)
Fax:
+49 (0)251 83 56874
Email: <a class="moz-txt-link-abbreviated" href="mailto:carsten.wolters@uni-muenster.de">carsten.wolters@uni-muenster.de</a>
Web: <a class="moz-txt-link-freetext" href="https://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/carsten-wolters/">https://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/carsten-wolters/</a></pre>
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