[FieldTrip] non-existent mat in BEM headmodel

[Ricardo Moura]

Hi Lilla,
Thank you very much for your reply.
It returns "mexglx", which is expected for a linux system, right?
I tried to change the path by my self in the ft_headmodel_dipoli but it
didnt work. Do you know how can I change it properly?

Best wishes
Ricardo


On 11 April 2013 16:40, Ricardo Moura <ricardoojm at gmail.com> wrote:

> 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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