[FieldTrip] Antw: Creating a head model using OPENMEEG - Intersecting mesh error

[Roey Schurr]

Otherwise, does anyone know if I could compute the leadfield using another
program and import it to fieldtrip?
Thank you once again,
Hoping to resolve this issue soon,
Roey


On Tue, Feb 18, 2014 at 3:16 PM, Roey Schurr <roeysc at gmail.com> wrote:

> Dear Daniel and all,
>
> First, thank you very much for your advice and codes. They have proved
> very helpful, and now I have obtained some very good brain-skull-scalp
> meshes!
>
> I am now having a problem using OPENMEEG to actually compute the leadfield
> based on these meshes, using the following code on frequency domain data:
>
>     cfg=[];
>     cfg.method  = 'dics';
>     cfg.elec = elec;
>     cfg.grid = grid;
>     cfg.vol = vol;
>     cfg.frequency = 10; % The mean frequency in the band
>     cfg.keepfilter  = 'yes';
>
>     sourceCombined = ft_sourceanalysis(cfg, freqCombined);
>
>
> The problem arises at the function "ft_leadfield_openmeeg" who tries
> using OPENMEEG installed on my PC (indeed there is a warning
> "warning('Sorry, Windows is not yet tested');" in this function).
> To fix onw of the bugs using a PC I changed line 94 to:
>
>     basefile = tempname;
>     [clearme basefile] = fileparts(basefile);
>     clear clearme;
>
> but even so, every line who tries to actually use OPENMEEG, such as line
> 149:
>
>     system([fullfile(OPENMEEG_PATH, 'om_check_geom'), ' -g ', geomFile])
>
> fails to do so.
> For instance, I get a Windows error window that says "om_assemble.exe has
> stopped working" and "om_minverser.exe has stopped working", and also:
>
> Computing inverse head matrix
>     187         system([fullfile(OPENMEEG_PATH, 'om_minverser'), ' ',
> hmFile, ' ', hminvFile]);
>     C:\OpenMEEG\bin\om_minverser version 2.1.0 (799) compiled at Aug 17
> 2011 19:50:11
>
>     | ------ C:\OpenMEEG\bin\om_minverser
>     |
> C:\Users\Roey\AppData\Local\Temp\ft-om\tp2f33a1b9_510f_4d55_805d_7ed6ce3b22e3_hm.bin
>     |
> C:\Users\Roey\AppData\Local\Temp\ft-om\tp2f33a1b9_510f_4d55_805d_7ed6ce3b22e3_hminv.bin
>     | -----------------------
>     Exception: Unable to open the file
> C:\Users\Roey\AppData\Local\Temp\ft-om\tp2f33a1b9_510f_4d55_805d_7ed6ce3b22e3_hm.bin
> for reading Doing my best....
>
> So it seems like OPENMEEG cannot open the file ending with "_hm.bin". This
> file indeed does no exist.
>
>
> I am using Matlab 2011b, full fieldtrip version of 17022014, Windows 7 64
> bit, and OPENMEEG with om_assemble version 2.1.0 (799) compiled at Aug 17
> 2011 19:50:41.
>
> Must I use a Macintosh or Linux computer to make this work?
>
> Any ideas would be greatly appreciated!
> Thank you very much in advance,
>
> Roey
>
>
> On Mon, Jan 20, 2014 at 8:10 PM, Daniel Wong <dan.wong.c at utoronto.ca>wrote:
>
>> You can try using the new iso2mesh meshing option that was recently added
>> by myself, Sarang Dalal, and Robert Oostenveld:
>>
>> cfg.method = 'iso2mesh';
>> cfg.numvertices = 10000;   % We'll decimate later - this gives nicer
>> results
>> bnd = ft_prepare_mesh(cfg,seg);
>>
>> % Decimate to a 1000, 2000, 3000 node mesh (scalp, skull, brain)
>> [bnd(1).pnt, bnd(1).tri] = meshresample(bnd(1).pnt, bnd(1).tri,
>> 1000/size(bnd(1).pnt,1));
>> [bnd(2).pnt, bnd(2).tri] = meshresample(bnd(2).pnt, bnd(2).tri,
>> 2000/size(bnd(2).pnt,1));
>> [bnd(3).pnt, bnd(3).tri] = meshresample(bnd(3).pnt, bnd(3).tri,
>> 3000/size(bnd(3).pnt,1));
>>
>> The latest version of OpenMEEG automatically fixes mesh orientations, but
>> if you have an older version of OpenMEEG, you'll need to set bnd(ii).tri =
>> bnd(ii).tri(:,[3 2 1]) to fix the orientation error that you'll get - at
>> least until we hard code that fix into FieldTrip.
>>
>> Also, assuming your meshes look like they should (use ft_plot_mesh to
>> check), if you still have a problem with meshes intersecting each other,
>> you will find a subfunction called decouplesurf that is temporarily stashed
>>  at the end of prepare_mesh_segmentation.m.  Copy this function into a new
>> m-file (decouplesurf.m) and use it to fix those intersections as follows:
>>
>> bnd = decouplesurf(bnd);
>>
>> Note, this will not fix self-intersections. If you're really having a bad
>> day, try using the iso2mesh toolbox meshcheckrepair function:
>> % Check and repair mesh
>> [bnd(ii).pnt, bnd(ii).tri] = meshcheckrepair(bnd(ii).pnt, bnd(ii).tri,
>> 'dup');
>> [bnd(ii).pnt, bnd(ii).tri] = meshcheckrepair(bnd(ii).pnt, bnd(ii).tri,
>> 'isolated');
>> [bnd(ii).pnt, bnd(ii).tri] = meshcheckrepair(bnd(ii).pnt, bnd(ii).tri,
>> 'deep');
>> [bnd(ii).pnt, bnd(ii).tri] = meshcheckrepair(bnd(ii).pnt, bnd(ii).tri,
>> 'meshfix');
>>
>> This info should eventually find its way onto the FieldTrip tutorial
>> pages...
>>
>>
>> Best Regards,
>> Daniel Wong
>>
>> Daniel Wong, PhD (IBBME, University of Toronto)
>> Postdoctoral Researcher
>> Department of Psychology
>> University of Konstanz
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
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