[FieldTrip] cfg.method = 'sam'

[Robert Oostenveld]

Dear Elena

The SAM implementation was contributed some time ago by Gareth Barnes, but apaprently went missing in the release version. I found the missing files in an older versionand just added them to the latest release version(*). Note that I did not test them for some time and also did not test them right now. It might be that you'll get follow up problems. If so, better report them on bugzilla.fcdonders.nl and not on the email list.

best regards,
Robert

PS (*) please download the FT version of this evening, which will include the beamformer_sam function which you need for cfg.method='sam' in ft_sourceanalysis.


 
On 3 Jun 2011, at 15:23, jan-mathijs schoffelen wrote:

> Hi Elena,
> 
> At some point we had an implementation for sam in FieldTrip. Apparently, this has been taken out of the release version. I don't know whether this was on purpose, or whether there was a good reason to do so.
> The reason you get an error is that the function is missing. We will look into the missing function issue.
> For the time being, you could try lcmv, which is very similar to sam.
> 
> Best,
> 
> Jan-Mathijs
> 
> 
> On Jun 3, 2011, at 2:57 PM, Elena Orekhova wrote:
> 
>> Dear colleagues,
>> Sorry, I posted much on the list recent time. I want to figure out how to run SAM analysis on my data.
>>  
>> When I run 'lcmv' beamformer on my averaged dataset it works fine:
>> cfg        = [];
>> cfg.grad            = hdr.grad;
>> cfg.method =  'lcmv';
>> cfg.grid   = grid;
>> cfg.vol    = vol_cm;
>> cfg.reducerank=2;
>> cfg.keepfilter = 'yes'
>> cfg.channel    = MAG; %MAG = {'MEG0721', 'MEG0731',... }
>> source  = ft_sourceanalysis(cfg, tlckavg);
>>  
>>  
>> When I do the same with   cfg.method =  'sam'  option,
>> I get the error:
>> *****************************
>> ??? Undefined function or method 'beamformer_sam' for input arguments of type 'struct'.
>>  
>> Error in ==> sourceanalysis at 1158
>>       dip(i) = beamformer_sam(grid, sens, vol, squeeze(avg(i,:,:)), squeeze(Cy(i,:,:)),
>>       optarg{:});
>>  
>> Error in ==> ft_sourceanalysis at 11
>> [varargout{1:nargout}] = funhandle(varargin{:});
>>  
>> Does anybody know how to make the ‘SAM’ option to work? 
>> Does anybody used cfg.method =  'sam'  option in the Fieldtrip???
>>  
>> Regards,
>> Elena
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> Dr. J.M. (Jan-Mathijs) Schoffelen 
> Donders Institute for Brain, Cognition and Behaviour, 
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: 0031-24-3614793
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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