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<p style="margin-top:0;margin-bottom:0">Many thanks Marios and Carsten - I will try out the scripts you sent me and let you know if I have any issues.</p>
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<p style="margin-top:0;margin-bottom:0">Best wishes</p>
<p style="margin-top:0;margin-bottom:0">Ravi</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Marios Antonakakis <antonakakismar@gmail.com><br>
<b>Sent:</b> Tuesday, November 6, 2018 8:21:56 AM<br>
<b>To:</b> Carsten Wolters<br>
<b>Cc:</b> fieldtrip@science.ru.nl; Ravi Mill<br>
<b>Subject:</b> Re: [FieldTrip] Incorporating White Matter conductivity anisotropy into FEM simbio</font>
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<div dir="ltr">Hi Ravi,
<div><br>
</div>
<div>assuming that you work under Linux and you have already the DTI data registered to MRI, you need then to run the below script.</div>
<div><br>
</div>
<div>
<div><b>%%1, calculate conductivity tensor for every voxel</b></div>
<div>% mri_segmented_final, V1, ... L1 variables have ft MRI structure</div>
<div><br>
</div>
<div> %skin,skull compacta, skull spongiosa, CSF, GM, WM</div>
<div>conductivity = [0.4300, 0.0024, 0.0086, 1.7900, 0.3300, 0.1400];<br>
</div>
<div>cfg =[];</div>
<div>cfg.compartments = mri_segmented_final.anatomylabel; % anatomical labels, skin: 0, skull spongiosa 2 and show on...</div>
<div>cfg.conductivity = conductivity;</div>
</div>
<div>[condcell, s, fail] = sb_calcTensorCond_tuch(cfg,mri_segmented_final,V1,V2,V3,L1,L2,L3); </div>
<div><br>
</div>
<div><b>%% 2. assign the conductivity tensor with the hex mesh </b></div>
<div>[mesh.nodes,mesh.elements,mesh.labels]= read_vista_mesh('foo_mesh.v);<br>
</div>
<div><br>
</div>
<div>
<div>mask = mri_segmented_final;</div>
<div>mask.anatomy((mask.anatomy~=5) & (mask.anatomy~=6))=0;<br>
</div>
<div>mask.anatomy((mask.anatomy==5) | (mask.anatomy==6))=1;</div>
</div>
<div><br>
</div>
<div>tensors = sb_assiTensorCond(mask,mesh.nodes,mesh.elements,mesh.labels,condcell);<br>
</div>
<div>write_vista_mesh('foo_mesh_aniso.v',mesh.nodes,mesh.elements,mesh.labels,tensors');<br>
</div>
<div><br>
</div>
<div>Do not hesitate to ask further questions.</div>
<div><i><br>
</i></div>
<div><i>*Note that write_vista_mesh and read_vista_mesh are private ft functions.</i></div>
<div><br>
</div>
<div>Best regards,</div>
<div> Marios</div>
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<div hspace="streak-pt-mark" style="max-height:1px"><img alt="" style="width:0px; max-height:0px; overflow:hidden" src="https://mailfoogae.appspot.com/t?sender=aYW50b25ha2FraXNtYXJAZ21haWwuY29t&type=zerocontent&guid=420ef8db-499e-48d0-b63b-37a4d6551822"><font color="#ffffff" size="1">ᐧ</font></div>
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<div dir="ltr">Στις Τρί, 6 Νοε 2018 στις 12:10 μ.μ., ο/η Carsten Wolters <<a href="mailto:carsten.wolters@uni-muenster.de" target="_blank">carsten.wolters@uni-muenster.de</a>> έγραψε:<br>
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<div class="x_m_2095508063422949630m_7826587823948522297moz-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="x_m_2095508063422949630m_7826587823948522297moz-txt-link-freetext" href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs10548-017-0568-9&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C9546e51982124567778d08d643eb0c3f%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636771074190746266&sdata=0V8kiAHNRSer1xqWNzPXDP4lZDk9UGk25eJzVGyasMY%3D&reserved=0" originalsrc="https://link.springer.com/article/10.1007/s10548-017-0568-9" shash="wQYJOI1OGRzrvJwqKgc+IYvXgCE8umrtQUhwjp3LYeKYwMVBgc/0iR8e8FDE2n3tyyfW+aK6jI7eB/BIPzdW5MjHX6k0Gnqm6b2WEUbJbGaqGuf80EDHCHIOqxczKs6W1uizza9wsYEcHEFWSm/lrNyEMO/zz9CGocAVNtIKXvI=" target="_blank">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>
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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://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffsl.fmrib.ox.ac.uk%2Ffsl%2Ffslwiki%2FFDT%2FUserGuide%23Processing_pipeline&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C9546e51982124567778d08d643eb0c3f%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636771074190756278&sdata=pMVolviUdbDljTvYcZpDYNu7qixY72mGJFgzTBk6KPQ%3D&reserved=0" originalsrc="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Processing_pipeline" shash="F6sEVLGcIKUEcwBP++dVa9fckAeEnuIlhZpIGBpoqqgUWDzx2YFc8vtZ6o5dJHMKL54n6bDrtlxxKsshDRvQf5sDB+U65INQITfWIYV7muGGYNP4f5jgq41Y8uUsrckD87mseCFyj7ptm+j3Ge/C+QHFLu4A14qqFjGo4qLgons=" class="x_m_2095508063422949630m_7826587823948522297OWAAutoLink" id="x_m_2095508063422949630m_7826587823948522297LPlnk529292" target="_blank">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>
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<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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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>
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<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>
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<div id="x_m_2095508063422949630m_7826587823948522297divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> fieldtrip
<a class="x_m_2095508063422949630m_7826587823948522297moz-txt-link-rfc2396E" href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">
<fieldtrip-bounces@science.ru.nl></a> on behalf of Johannes Vorwerk <a class="x_m_2095508063422949630m_7826587823948522297moz-txt-link-rfc2396E" href="mailto:j.vorw01@gmail.com" target="_blank">
<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>
<div style="word-wrap:break-word">Dear Ravi,
<div><br>
</div>
<div>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><br>
</div>
<div>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><br>
</div>
<div>Best,</div>
<div><span class="x_m_2095508063422949630m_7826587823948522297x_Apple-tab-span" style="white-space:pre-wrap"></span>Johannes</div>
<div><br>
</div>
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<blockquote type="cite">
<div>Am 29.10.2018 um 12:31 schrieb Carsten Wolters <<a href="mailto:carsten.wolters@uni-muenster.de" class="x_m_2095508063422949630m_7826587823948522297OWAAutoLink" id="x_m_2095508063422949630m_7826587823948522297LPlnk144193" target="_blank">carsten.wolters@uni-muenster.de</a>>:</div>
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Dear Ravi,<br>
<br>
1) You can use the pure SimBio-code from<span class="x_m_2095508063422949630m_7826587823948522297x_Apple-converted-space"> </span><br>
<a class="x_m_2095508063422949630m_7826587823948522297x_moz-txt-link-freetext x_m_2095508063422949630m_7826587823948522297OWAAutoLink" 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%7C9546e51982124567778d08d643eb0c3f%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636771074190776294&sdata=rlLOQYHDMLXgHD3OI023GbYYBFdrfc1vhw80FMrxysg%3D&reserved=0" originalsrc="https://www.mrt.uni-jena.de/simbio/index.php/Main_Page" shash="cDHTef4aq5cUNT20RubJps18MloEwX0qVhgu14I6dJfFPKcK3yCooG2Zl45ntlVIVVGgJHj2ylQGbhnrowMIeeK7C6qkrGrDW2qPEn7D5EQ1fAkmrwyiFrVKvpHnJA3qxBeB6Lbcs/eJz7xamB19XcVv9ZGNjWcHZuKOOXv5ABQ=" id="x_m_2095508063422949630m_7826587823948522297LPlnk649518" target="_blank">https://www.mrt.uni-jena.de/simbio/index.php/Main_Page</a><br>
to treat WM anisotropy.<br>
While it would in principle also be possible to use anisotropic conductivities with FieldTrip-SimBio,<span class="x_m_2095508063422949630m_7826587823948522297x_Apple-converted-space"> </span><br>
this is currently not implemented using ft_prepare_headmodel. Johannes (in CC), who implemented<span class="x_m_2095508063422949630m_7826587823948522297x_Apple-converted-space"> </span><br>
Fieldtrip-SimBio, answered a same question by Junjie Wu in March 2018:<span class="x_m_2095508063422949630m_7826587823948522297x_Apple-converted-space"> </span><br>
"Depending on your matlab skills and your available time, I could help you to give it a<span class="x_m_2095508063422949630m_7826587823948522297x_Apple-converted-space"> </span><br>
try though. It should be possible with using some direct function calls instead of the high-level fieldtrip-functions."<br>
<br>
2) We recommend<span class="x_m_2095508063422949630m_7826587823948522297x_Apple-converted-space"> </span><br>
<a class="x_m_2095508063422949630m_7826587823948522297x_moz-txt-link-freetext x_m_2095508063422949630m_7826587823948522297OWAAutoLink" 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%7C9546e51982124567778d08d643eb0c3f%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636771074190776294&sdata=NwqVxmn1XFHEMKNFih%2FyGKqzOxuc09l4q%2Fzo6oPKFz4%3D&reserved=0" originalsrc="http://www.sci.utah.edu/~wolters/PaperWolters/2012/RuthottoEtAl_PhysMedBiol_2012.pdf" shash="kINJ2s0a85VTXMcGldfHFcwN6CsfDGn+cxbuVVU6MF1eHP7LViASfjHhaSxw6owZ9XvsMfmiTiL1HjRDDki8x3W4GiTkOZduQYugVmc6/t3H4kILMge6htse1ztwyK5SWSGNHZe2MKVp0cmISTcSZFtziM0rLvFcXIcEeeDMrQs=" id="x_m_2095508063422949630m_7826587823948522297LPlnk912676" target="_blank">http://www.sci.utah.edu/~wolters/PaperWolters/2012/RuthottoEtAl_PhysMedBiol_2012.pdf</a><br>
on individual data. I could imagine that an atlas does a reasonable job w.r.t. the main<br>
bigger fiber tracts such as corpus callosum or pyramidal tracts, but that the finer details<br>
in the cortices are individual. We always measure T1, T2 and DTI from each subject<br>
and I personally do not have experience with such a group-level anisotropy compared<span class="x_m_2095508063422949630m_7826587823948522297x_Apple-converted-space"> </span><br>
to the individual one. Might be interesting to hear from others what they think!?<br>
<br>
BR<br>
Carsten<br>
<br>
<br>
<br>
Am 25.10.18 um 23:05 schrieb Ravi Mill:<br>
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<div style="margin-top:0px; margin-bottom:0px">Dear Fieldtrippers</div>
<div style="margin-top:0px; margin-bottom:0px"><br>
</div>
<div style="margin-top:0px; margin-bottom:0px">I have applied the FEM simbio head modeling pipeline implemented in Fieldtrip to my EEG data. <span>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%7C9546e51982124567778d08d643eb0c3f%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636771074190786303&sdata=uzIHxDZ985MawVWXs3wIEPKQzflY8K45fheAeVamaEo%3D&reserved=0" originalsrc="https://doi.org/10.1016/j.neuroimage.2014.06.040" shash="dk/VYshtxsj4/atlUZKqCGxQHi/SlWvoYRgrKL74kXuv2mRjfBCuR2oGbODC5fdxxzuj6Lizj1/++ryySBpqC9oi6KiWgrrG86kPMLMSjQgQ871gCbBAZc4qY7fUFEeUfjJCy67c0RNRwDD7mwfSeSAaQsA/nir7GiSb0tQFimM=" class="x_m_2095508063422949630m_7826587823948522297x_OWAAutoLink" id="x_m_2095508063422949630m_7826587823948522297LPlnk216235" target="_blank">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 style="font-size:12pt">My questions
are as follows:</span></div>
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</span></div>
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<li>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>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%7C9546e51982124567778d08d643eb0c3f%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636771074190796311&sdata=%2BnHcr2pce3FTYJhfLl21L1UuybVN9M0X8I%2BjvidmwAI%3D&reserved=0" originalsrc="https://www.mrt.uni-jena.de/simbio/index.php/SIMBIO/Releasenotes/Examples" shash="FaVEkQ2p8frMMzradkQ+TX/oK3HPw/Ew93w/Saehn9Xe7D/q45lGXaXoOuFbzg9JQF2c1V6owDyMFKtpenQEguigVFCX4ymDoE38J7xej9K8+I0zA0jgQ/SysjRbII5lPkY2PCoCmFlCFYR2DIKN2imdfcS92K8WYK8hBVwNjtA=" class="x_m_2095508063422949630m_7826587823948522297x_OWAAutoLink" id="x_m_2095508063422949630m_7826587823948522297LPlnk493580" target="_blank">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>
<div style="margin-top:0px; margin-bottom:0px">Any help would be greatly appreciated!</div>
<div style="margin-top:0px; margin-bottom:0px"><br>
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<div style="margin-top:0px; margin-bottom:0px">Thanks</div>
<div style="margin-top:0px; margin-bottom:0px">Ravi</div>
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<pre class="x_m_2095508063422949630m_7826587823948522297x_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_m_2095508063422949630m_7826587823948522297x_moz-txt-link-abbreviated x_m_2095508063422949630m_7826587823948522297OWAAutoLink" href="mailto:carsten.wolters@uni-muenster.de" id="x_m_2095508063422949630m_7826587823948522297LPlnk155336" target="_blank">carsten.wolters@uni-muenster.de</a>
Web: <a class="x_m_2095508063422949630m_7826587823948522297x_moz-txt-link-freetext x_m_2095508063422949630m_7826587823948522297OWAAutoLink" 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%7C9546e51982124567778d08d643eb0c3f%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636771074190816327&sdata=nSKW70cIZRqhjpSqwitcFCGEM%2B14FMhN6j9iF2zd7wM%3D&reserved=0" originalsrc="https://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/carsten-wolters/" shash="bEmxHZk9TzRxsZ3bwXGUVEt2WBbQQizJxjG7/OqkA6T0D99IPHCvFXU92SJfdMzMWa86HWUdDUJggQ+ZjX+xTa4BhRuRvDIlQyvricsH8nFucXMa5wwLEl/YPB3W+Yb+3Q5nSxqXqzgdKhqKtD44aDgaSgJBrQK8Vf9eRDVgV3w=" id="x_m_2095508063422949630m_7826587823948522297LPlnk782212" target="_blank">https://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/carsten-wolters/</a></pre>
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<pre class="x_m_2095508063422949630m_7826587823948522297moz-signature" cols="72">--
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_m_2095508063422949630m_7826587823948522297moz-txt-link-abbreviated" href="mailto:carsten.wolters@uni-muenster.de" target="_blank">carsten.wolters@uni-muenster.de</a>
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