[FieldTrip] More: lead field Cholesky....

[RICHARDS, JOHN]

I solved this problem on my windows computers.  Now when I run the same program on a Linux machine, I get the same output.

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.

My linux is Red Hat 7, MATLAB is the 2014a, FT is the 2/14/15 download.

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.

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;

Thanks, John

***********************************************
John E. Richards
Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC  29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: richards-john at sc.edu<applewebdata://7FD23341-F720-46A5-97FD-B4149780F9D4/richards-john@sc.edu>
HTTP: jerlab.psych.sc.edu
*************************************************
[cid:75EDAFDB-FCB8-4E5C-A9A4-4A2E0A1B56B7]

From: <RICHARDS>, John Richards <richards at mailbox.sc.edu<mailto:richards at mailbox.sc.edu>>
Date: Monday, February 16, 2015 at 8:37 AM
To: "fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>" <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: lead field Cholesky....

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.

Thanks in advance for your consideration.

John

***********************************************
John E. Richards Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC  29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: richards-john at sc.edu<mailto:richards-john at sc.edu>
HTTP: jerlab.psych.sc.edu
***********************************************


From: <RICHARDS>, John Richards <richards at mailbox.sc.edu<mailto:richards at mailbox.sc.edu>>
Date: Sunday, February 15, 2015 at 12:26 AM
To: "fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>" <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: lead field Cholesky....

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: http://fieldtrip.fcdonders.nl/development/simbio.  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.

Any help on this?

John


using headmodel specified in the configuration
using electrodes specified in the configuration
Find electrode positions...
Calculate transfer matrix...
Electrode 2 of 128
Scaling stiffnes matrix...
Preconditioning...
Could not compute incomplete Cholesky-decompositon. Rescaling stiffness matrix…

error using ichol
Input must be structurally nonsingular with structurally nonzero diagonal.

Error in sb_solve (line 33)
    L = ichol(L);

Error in sb_calc_vecx (line 12)
vecx = sb_solve(stiff,vecb);

Error in sb_transfer (line 40)
    transfer(i,:) = sb_calc_vecx(vol.stiff,vecb,vol.elecnodes(1));

Error in ft_prepare_vol_sens (line 500)
      vol.transfer = sb_transfer(vol,sens);

Error in prepare_headmodel (line 94)
[vol, sens] = ft_prepare_vol_sens(vol, sens, 'channel', cfg.channel, 'order',
cfg.order);

Error in ft_prepare_leadfield (line 137)
[vol, sens, cfg] = prepare_headmodel(cfg, data);




***********************************************
John E. Richards Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC  29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: richards-john at sc.edu<mailto:richards-john at sc.edu>
HTTP: jerlab.psych.sc.edu
***********************************************

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150216/f37482c3/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 0E9D0CE7-F37D-4858-BC01-79FD2F2554B1[1].png
Type: image/png
Size: 30144 bytes
Desc: 0E9D0CE7-F37D-4858-BC01-79FD2F2554B1[1].png
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150216/f37482c3/attachment-0001.png>