[FieldTrip] non-existent mat in BEM headmodel

[Lilla.Magyari at mpi.nl]

hi Ricardo,

I'd change forward/ft_headmodel_dipoli.m
in line 134
from this:
case {'mexglnx86' 'mexa64'}

to this:
case {'mexglnx86' 'mexa64' 'mexglx'}

Please, try this first, and if it is still not working, it is possible 
that you should compile it yourself. If that still doesn't work out,
please, send a message to the bugzilla.
http://bugzilla.fcdonders.nl/

And if you could run it, please, also give us a feedback about it.
Thanks.

Best,

Lilla


> 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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