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<div>I solved this problem on my windows computers. Now when I run the same program on a Linux machine, I get the same output.</div>
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<div>I note that with the windows computer I had to add the MS Visual C++ 2008 redistributable and the Intel Visual Fortran redistributable libraries. I found in another post that someone said these libraries are unnecessary on Linux, I presume that means
either these libraries exist on Linux already, or that they use a different library for these functions.</div>
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<div>My linux is Red Hat 7, MATLAB is the 2014a, FT is the 2/14/15 download.</div>
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<div>I realize this may be a question for the simbio development group, if so would you let me know and I will try to contact that group.</div>
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<div>By the way the models are a five segmented head (wm, gm, csf, skull, scalp) or fully segmented head (the former + eyes, nasal cavity, head-muscle, ….); the electrodes are co-registered with the MRI outside of FT so they fit correctly on the scalp; </div>
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<div>Thanks, John</div>
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<div><span class="Apple-style-span" style="font-family: 'Times New Roman', serif; font-size: 16px;"><span style="font-size: 10pt; font-family: Consolas;">***********************************************<br>
John E. Richards<br>
Carolina Distinguished Professor<br>
Department of Psychology<br>
University of South Carolina<br>
Columbia, SC 29208<br>
Dept Phone: 803 777 2079<br>
Fax: 803 777 9558<br>
Email: </span><u><span style="font-size: 10pt; font-family: Consolas; color: blue; "><a href="applewebdata://7FD23341-F720-46A5-97FD-B4149780F9D4/richards-john@sc.edu" style="color: blue;">richards-john@sc.edu</a><br>
</span></u><span style="font-size: 10pt; font-family: Consolas;">HTTP: jerlab.psych.sc.edu<br>
*********************************************<span class="apple-style-span">****</span><br>
</span><span style="font-size: 11pt; font-family: Calibri, sans-serif;"><img border="0" width="480" height="101" id="_x0000_i1025" src="cid:75EDAFDB-FCB8-4E5C-A9A4-4A2E0A1B56B7" type="image/png"></span></span></div>
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<span style="font-weight:bold">From: </span><RICHARDS>, John Richards <<a href="mailto:richards@mailbox.sc.edu">richards@mailbox.sc.edu</a>><br>
<span style="font-weight:bold">Date: </span>Monday, February 16, 2015 at 8:37 AM<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>" <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
<span style="font-weight:bold">Subject: </span>Re: lead field Cholesky....<br>
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<div>Update on this. I may have solved my own problem. I had “nasal cavity” with an assigned conductivity of 0. I changed this to a very small value, and it passed this step at least once. I will let you know if this happens again. </div>
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<div>Thanks in advance for your consideration.</div>
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<div>John</div>
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<div style="font-family: Consolas; font-size: medium;">***********************************************</div>
<div style="font-family: Consolas; font-size: medium;">John E. Richards Carolina Distinguished Professor</div>
<div style="font-family: Consolas; font-size: medium;">Department of Psychology</div>
<div style="font-family: Consolas; font-size: medium;">University of South Carolina</div>
<div style="font-family: Consolas; font-size: medium;">Columbia, SC 29208</div>
<div style="font-family: Consolas; font-size: medium;">Dept Phone: 803 777 2079</div>
<div style="font-family: Consolas; font-size: medium;">Fax: 803 777 9558</div>
<div style="font-family: Consolas; font-size: medium;">Email: <a href="mailto:richards-john@sc.edu">richards-john@sc.edu</a></div>
<div style="font-family: Consolas; font-size: medium;">HTTP: jerlab.psych.sc.edu</div>
<div style="font-family: Consolas; font-size: medium;">***********************************************</div>
<div style="font-family: Consolas; font-size: medium;"><br>
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<span style="font-weight:bold">From: </span><RICHARDS>, John Richards <<a href="mailto:richards@mailbox.sc.edu">richards@mailbox.sc.edu</a>><br>
<span style="font-weight:bold">Date: </span>Sunday, February 15, 2015 at 12:26 AM<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>" <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
<span style="font-weight:bold">Subject: </span>lead field Cholesky....<br>
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<div>I am just starting to try field trip, and want to do EEG/ERP source modeling with FEM models. I am trying to create a FEM model with the simbio method. I am following the tutorial:
<a href="http://fieldtrip.fcdonders.nl/development/simbio">http://fieldtrip.fcdonders.nl/development/simbio</a>. I have a fully segmented head model (gm, wm, csf, eyes, skull,….) and get almost all the way through the methods; including seeing figures that
suggest things are going in correctly. At the last step to prepare the lead field, I get the following output (and error): Could not compute incomplete Cholesky-decompositon. Rescaling stiffness matrix (full output below). I understand in principle the Cholesky-decomposition
and why it is used, the rescaling, where this is happening in the sb_solve.m, etc However, I don’t know what to do with my model to get this to work. I have tried a simpler model (fewer segments), a smaller head (full head, vs MNI-type-size head), and a
few other things, none of them work.</div>
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<div>Any help on this?</div>
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<div>John</div>
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<div>using headmodel specified in the configuration</div>
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<div>using electrodes specified in the configuration</div>
<div>Find electrode positions...</div>
<div>Calculate transfer matrix...</div>
<div>Electrode 2 of 128</div>
<div>Scaling stiffnes matrix...</div>
<div>Preconditioning...</div>
<div>Could not compute incomplete Cholesky-decompositon. Rescaling stiffness matrix…</div>
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<div>error using ichol</div>
<div>Input must be structurally nonsingular with structurally nonzero diagonal.</div>
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<div>Error in sb_solve (line 33)</div>
<div> L = ichol(L);</div>
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<div>Error in sb_calc_vecx (line 12)</div>
<div>vecx = sb_solve(stiff,vecb);</div>
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<div>Error in sb_transfer (line 40)</div>
<div> transfer(i,:) = sb_calc_vecx(vol.stiff,vecb,vol.elecnodes(1));</div>
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<div>Error in ft_prepare_vol_sens (line 500)</div>
<div> vol.transfer = sb_transfer(vol,sens);</div>
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<div>Error in prepare_headmodel (line 94)</div>
<div>[vol, sens] = ft_prepare_vol_sens(vol, sens, 'channel', cfg.channel, 'order',</div>
<div>cfg.order);</div>
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<div>Error in ft_prepare_leadfield (line 137)</div>
<div>[vol, sens, cfg] = prepare_headmodel(cfg, data);</div>
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<div style="font-family: Consolas; font-size: medium;">***********************************************</div>
<div style="font-family: Consolas; font-size: medium;">John E. Richards Carolina Distinguished Professor</div>
<div style="font-family: Consolas; font-size: medium;">Department of Psychology</div>
<div style="font-family: Consolas; font-size: medium;">University of South Carolina</div>
<div style="font-family: Consolas; font-size: medium;">Columbia, SC 29208</div>
<div style="font-family: Consolas; font-size: medium;">Dept Phone: 803 777 2079</div>
<div style="font-family: Consolas; font-size: medium;">Fax: 803 777 9558</div>
<div style="font-family: Consolas; font-size: medium;">Email: <a href="mailto:richards-john@sc.edu">richards-john@sc.edu</a></div>
<div style="font-family: Consolas; font-size: medium;">HTTP: jerlab.psych.sc.edu</div>
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