[FieldTrip] non-existent mat in BEM headmodel

[Ricardo Moura]

Hi,

I had to re-install ubuntu in order to provide more space for the analysis
(since I was having the problem with the temporary files, which might have
been too large for my ubuntu partition).
But now the problem I have with the "ft_prepare_headmodel" is even weirder
than before. The program now is complaining that there is no dipoli for my
system:


cfg        = [];
cfg.method ='dipoli';
vol        = ft_prepare_headmodel(cfg, segmentedmri);



??? Error using ==> ft_headmodel_dipoli at 138
there is no dipoli executable for your platform

Error in ==> ft_prepare_headmodel at 226
      vol =
ft_headmodel_dipoli(geometry,'conductivity',cfg.conductivity,'isolatedsource',cfg.isolatedsource);


I am running this script in a 2010b matlab version, installed in ubuntu
12.04. It should be working fine, right?

Thanks in advance,
Ricardo


On 28 March 2013 14:39, Ricardo Moura <ricardoojm at gmail.com> wrote:

> Hi Jörn,
> thank you very much for your response!
> I checked the segmentation and everything seems to be ok (as far as I can
> say... No error messages were shown during the processing and I checked the
> generated objects and plots).
>
> But I had a strange error while preparing the head model. Somehow the
> command cannot find the dipoli files, even thought they are really where
> they should be. And the second message
> ("/tmp/tp2619f3f3_574d_478a_bfbb_01193b4f8e0c.ama'") I really have no clue
> of what it means.
>
> And I am running this command on a ubuntu 12.04 32-bit.
>
> Do you have any idea of how I can solve it?
>
> Thanks once again,Best,
> Ricardo
>
> using the executable
> "/usr/local/MATLAB/R2012a/toolbox/fieldtrip-20130314/external/dipoli/dipoli"
> /tmp/tpd4e382c9_74a1_402d_be1a_6d2c82e749cc.sh: 3:
> /tmp/tpd4e382c9_74a1_402d_be1a_6d2c82e749cc.sh:
> /usr/local/MATLAB/R2012a/toolbox/fieldtrip-20130314/external/dipoli/dipoli:
> not found
> Warning: an error ocurred while running dipoli
> > In ft_headmodel_dipoli at 201
>   In ft_prepare_headmodel at 226
>
> Error using fread
> Invalid file identifier.  Use fopen to generate a valid file identifier.
> Warning: File '/tmp/tp2619f3f3_574d_478a_bfbb_01193b4f8e0c.ama' not found.
> > In ft_headmodel_dipoli at 209
>   In ft_prepare_headmodel at 226
>
>
> On 27 March 2013 13:10, Ricardo Moura <ricardoojm at gmail.com> wrote:
>
>> Dear all
>> I am creating a BEM model for eeg, following the appropriate tutorial,
>> but I have a problem when preparing the headmodel. The output I have from
>> the ft_prepare_headmodel command does not contain the "mat", and so, when I
>> try to generate the leadfield, it returns an error message due to non
>> existent "mat". I saw that other users had similar problem, but I haven't
>> found a solution though. So, what is wrong with my script?
>>
>> Thanks a lot in advance!
>> Best,
>> Ricardo
>>
>>
>>
>>
>> load standard_mri.mat
>> mri_orig=mri;
>> disp(mri)
>>
>> % Segmenting the data
>> cfg = [];
>> cfg.output= {'scalp','skull','brain'};
>> segmentedmri  = ft_volumesegment(cfg, mri_orig);
>> disp(segmentedmri)
>> save segmentedmri segmentedmri
>>
>> % MESH
>> cfg=[];
>> cfg.tissue={'brain','skull','scalp'};
>> cfg.numvertices = [3000 2000 1000];
>> bnd=ft_prepare_mesh(cfg,segmentedmri);
>> disp(bnd(1))
>>
>> % Head Model = variavel vol
>> cfg        = [];
>> cfg.method ='bem_dipoli'; %dipoli singlesphere
>> vol        = ft_prepare_headmodel(cfg, segmentedmri);
>>
>>
>> >> disp(vol)
>>              bnd: [1x3 struct]
>>             cond: [0.3300 0.0041 0.3300]
>>     skin_surface: 1
>>           source: 3
>>             type: 'dipoli'
>>             unit: 'mm'
>>              cfg: [1x1 struct]
>>
>>
>>
>>
>
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