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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear all,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks for the helpful replies! I have just tried, and it indeed runs fine when you specify 4 conductivity. Guess I
was confused by the specific error message: “</span><span lang="EN-US" style="font-family:"Helvetica","sans-serif";color:black">More than 3 shells not allowed</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">”.
Perhaps this message can be made more accurate: “</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">Conductivity values need to be explicitly specified when using 2 shells or more than 3 shells.</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">”.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Regards, Martijn<i><o:p></o:p></i></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-bounces@science.ru.nl [mailto:fieldtrip-bounces@science.ru.nl]
<b>On Behalf Of </b>Maité Crespo García<br>
<b>Sent:</b> donderdag 19 november 2015 17:58<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] Number of shells in OpenMEEG<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" style="background:white"><span style="font-size:10.5pt;font-family:"Helvetica","sans-serif";color:black">Dear Martijn,<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.5pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.5pt;font-family:"Helvetica","sans-serif";color:black">the error happens when you don't specify the conductivity values.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.5pt;font-family:"Helvetica","sans-serif";color:black">Best,<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.5pt;font-family:"Helvetica","sans-serif";color:black">Maite<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";color:black">El Jueves 19 de noviembre de 2015 14:07, Sarang S. Dalal <<a href="mailto:sarang.dalal@uni-konstanz.de">sarang.dalal@uni-konstanz.de</a>>
escribió:</span><span style="font-family:"Helvetica","sans-serif";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt;background:white"><span style="font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt;background:white"><span style="font-family:"Helvetica","sans-serif";color:black">Dear Martijn,<br>
<br>
Our group routinely computes 4-layer BEM models, but we have written a new pipeline (already implemented within the official FieldTrip pipeline) to effectively replace ft_headmodel_openmeeg. Unfortunately we still need to complete the documentation, but below
is an example of how to call it.<br>
<br>
BTW, I am currently comparing the performance between 4-layer and 3-layer BEM for my own MEG data. It seems that 4-layer (i.e., with CSF) might increase the chances of spurious voxels near the brain surface; however, this could be due to imperfect segmentation
or sharp edges still present in my surfaces.<br>
<br>
I hope this helps,<br>
Sarang<br>
<br>
<br>
<br>
subjId = 'test';<br>
vol.type = 'openmeeg';<br>
vol.basefile = subjId;<br>
vol.path = ['./' subjId '/hm/openmeeg_out']; % following files in here can be reused across sessions for same participant: hm.bin, hm_inv.bin, dsm.bin<br>
vol.bnd = bnd;<br>
switch(length(bnd)) % the number of layers in “bnd” determines whether to use 4-layer or 3-layer<br>
case 4<br>
vol.cond = [0.33 0.0041 1.79 0.33]; % scalp skull CSF brain<br>
case 3<br>
vol.cond = [0.33 0.0041 0.33]; % scalp skull brain (no CSF)<br>
end<br>
vol = ft_convert_units(vol,'mm'); % we do everything in MRI mm space<br>
<br>
% we prefer to do all computations in MRI mm space, so sensor positions need to be transformed<br>
grad = data.grad;<br>
grad_mm = ft_convert_units(grad,'mm');<br>
grad_mri = ft_transform_sens(coreg.meg2mri_tfm, grad_mm); % transforms the grad coordinates to mri coordinates % this is custom for our group; you may have an alternative way<br>
<br>
<br>
cfg = [];<br>
cfg.grad = grad_mri;<br>
cfg.grid.warpmni = 'yes';<br>
load standard_sourcemodel3d10mm; % loads in sourcemodel (i.e., MNI voxel grid)<br>
sourcemodel = ft_convert_units(sourcemodel,'mm');<br>
cfg.grid.template = sourcemodel;<br>
cfg.grid.nonlinear = 'yes'; % use non-linear normalization<br>
cfg.mri = mri;<br>
cfg.unit = 'mm',<br>
<br>
cfg.vol = vol;<br>
cfg.channel = channel;<br>
cfg.reducerank = 'no';<br>
cfg.grid.resolution = 5; % in mm<br>
grid = ft_prepare_leadfield(cfg);<br>
<br>
<br>
<br>
<br>
<br>
> Message: 9<br>
> Date: Thu, 19 Nov 2015 10:53:55 +0100<br>
> From: Alexandre Gramfort <<a href="mailto:alexandre.gramfort@telecom-paristech.fr">alexandre.gramfort@telecom-paristech.fr</a>><br>
> To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
> Subject: Re: [FieldTrip] Number of shells in OpenMEEG<br>
> Message-ID:<br>
> <CADeotZrk4zSGstuFMJ=WEKqYCQVqMkFR9SBkhzQUP=<a href="mailto:XCHSAOyg@mail.gmail.com">XCHSAOyg@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset=UTF-8<br>
> <br>
> hi,<br>
> <br>
> I confirm that OpenMEEG can handle more than 3 layers.<br>
> <br>
> Best,<br>
> Alex<br>
> <br>
> <br>
> On Thu, Nov 19, 2015 at 9:58 AM, Martijn Vlaar - 3ME<br>
> <<a href="mailto:M.P.Vlaar@tudelft.nl">M.P.Vlaar@tudelft.nl</a>> wrote:<br>
>> Dear all,<br>
>> <br>
>> <br>
>> <br>
>> I am interested in including the CSF in the forward model.<br>
>> <br>
>> <br>
>> <br>
>> In ft_headmodel_openmeeg at line 75 there is an error message: ?More than 3<br>
>> shells not allowed?. In the OpenMEEG documentation I do not find such a<br>
>> limitation.<br>
>> <br>
>> <br>
>> <br>
>> Could someone clarify why the OpenMEEG-related function in fieldtrip is<br>
>> restricted to 1, 2 or 3 shells?<br>
>> <br>
>> <br>
>> <br>
>> Thank you in advance!<br>
>> <br>
>> <br>
>> <br>
>> Martijn Vlaar<br>
>> <br>
>> <br>
>> <br>
>> ________________________________<br>
>> <br>
>> Ir. Martijn Vlaar<br>
>> <br>
>> Delft University of Technology<br>
>> <br>
>> BioMechanical Engineering<br>
>> <br>
>> Mekelweg 2, 2628 CD Delft, The Netherlands<br>
>> <br>
>> tel: +31 (0)1527 85625<br>
>> <br>
>> fax: +31 (0)1527 84717<br>
>> <br>
>> mobile: +31 (0)618081635<br>
>> <br>
>> <br>
>> <br>
>> <br>
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