[FieldTrip] Fwd: Modification of ft_timelockgrandaverage cfg.keepindividual
jan-mathijs schoffelen
jan.schoffelen at donders.ru.nl
Thu Feb 10 13:15:57 CET 2011
Dear Lucie,
Thank you very much for your feedback. I take the liberty to anyhow
post this to the discussion list, so that other people may take
notice / join in the discussion / etc.
> Thanks a lot for this quick response : I understand the logic behind
> this. It's true that I noticed some inconsistencies due to the
> interpretation of the field dimord which can't be well defined if
> you have both individual and average data in your structure.
OK
> However, I think many people were happy with this option as it was.
> It's quite handy to keep both the average and individual data
> because you can compute statistics and at the same time you don't
> have to redo the average every time. I think a lot of scripts rely
> on that at least in our lab.
The historical purpose for supporting cfg.keepindividual = 'yes', was
in order to get a representation of all single subjects' data in a
single data matrix: data.individual. Nowadays, ft_timelockstatistics
supports multiple data structures in the input, i.e.
ft_timelockstatistics(cfg, subj1, subj2 subj3, etc) so I think the
call to ft_timelockgrandaverage could even be bypassed.
The FieldTrip development team is very keen on providing backward
compatibility support. While in general this is feasible for the
functions which are in FieldTrip, it is very difficult to realize for
lab-specific scripts. In this particular example I think that clarity
of the data representation should prevail over backward compatibility
issues, particularly because in this case there's an easy workaround:
just call ft_timelockgrandaverage twice. Moreover, a clean and
unambiguous data representation is a prerequisite for further
developing the software, and keeping the historical 'oddity' will only
hamper code development.
> Furthermore, it's a bit strange to have a function called
> ft_timelockgrandaverage which doesn't compute any grandaverage in
> some cases !
I agree, yet see my point above. Some people may just like to have the
data represented in a single matrix.
>
> I would suggest to keep the function as it is but add more options
> (such as cfg.dimord = 'avg' or 'individual') to make the
> experimenter aware of this issue and to solve further computation
> problem.
I hope I could convince you that our philosophy makes sense and that
you and your lab-mates are willing to make the effort of adjusting the
scripts a bit for future analyses. If very problematic, I would advice
for the current analyses to rely on an old version of
ft_timelockgrandaverage.
Best wishes,
Jan-Mathijs
> Thank you again,
>
> Lucie
>
> PS : I've sent this email only to you as this is just a suggestion
> which might not be relevant for all users.
>
>
> 2011/2/10 jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
> Dear Lucie,
>
> Yes, indeed this has recently been changed. The logic behind it is
> the following:
>
> One either typically wants to keep the individuals, OR the average.
>
> If in your case you need the average, you have to specify
> cfg.keepindividual = 'no';
>
> Keeping both the average and the individual leads to an inconsistent
> definition of the data structure.
> The field 'dimord' does not allow for an unequivocal interpretation
> of both indidual and avg are present.
>
> If you need both the individual, and the avg, you now need to run
> ft_timelockgrandaverage twice, once with cfg.keepinididual = 'yes',
> and once with cfg.keepindividual = 'no';
>
> Best wishes,
>
> Jan-Mathijs
>
>
> On Feb 10, 2011, at 11:58 AM, Lucie Charles wrote:
>
>> Hello everyone,
>>
>> It seems that there has been a modification of
>> ft_timelockgrandaverage : now if you specify cfg.keepindividual =
>> 'yes', the grandaverage is computed but is not included in the
>> output of the function (see above).
>>
>> Why is that ? Many of my scripts rely on this option and I wanted
>> to know if there was a good reason for it.
>>
>> Thanks,
>>
>> Lucie
>>
>> New version of ft_timelockgrandaverage (downloaded yesterday), line
>> 159-176
>>
>> %--------------------------------------------
>> % % collect the results
>> %--------------------------------------------
>>
>> grandavg = [];
>> grandavg.label = cfg.channel; % cell-array
>> %grandavg.fsample = varargin{1}.fsample; % fsample is obsolete
>> grandavg.time = ResultsTime; % 1 x Nsamples
>>
>> %KEEP INDIVIDUAL MEANS?
>> if strcmp(cfg.keepindividual, 'yes')
>> grandavg.individual = avgmat; % Nsubj x Nchan x Nsamples
>> grandavg.dimord = 'subj_chan_time';
>> else
>> grandavg.avg = ResultGrandavg; % Nchan x Nsamples
>> grandavg.var = ResultVar; % Nchan x Nsamples
>> grandavg.dimord = 'chan_time';
>> end
>>
>> Older version of ft_timelockgrandaverage (april 2010)
>>
>> %--------------------------------------------
>> % % collect the results
>> %--------------------------------------------
>>
>> %SWITCH CHANNEL TO LABEL?
>> grandavg.label = cfg.channel; % cell-array
>> grandavg.fsample = varargin{1}.fsample;
>> grandavg.avg = ResultGrandavg; % Nchan x Nsamples
>> grandavg.var = ResultVar; % Nchan x Nsamples
>> grandavg.time = ResultsTime; % 1 x Nsamples
>>
>> %KEEP INDIVIDUAL MEANS?
>> if strcmp(cfg.keepindividual, 'yes')
>> grandavg.individual = avgmat; % Nsubj x Nchan x Nsamples
>> grandavg.dimord = 'subj_chan_time';
>> else
>> grandavg.dimord = 'chan_time';
>> end
>>
>>
>> --
>> Lucie CHARLES
>>
>> INSERM-CEA Cognitive Neuroimaging unit
>>
>> CEA/SAC/DSV/DRM/NeuroSpin
>> Bât 145, Point Courrier 156
>> F-91191 Gif/Yvette, FRANCE
>> Tel : +33 1 69 08 99 74
>> Fax : +33 1 69 08 79 73
>> _______________________________________________
>> 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
>
>
>
> --
> Lucie CHARLES
>
> INSERM-CEA Cognitive Neuroimaging unit
>
> CEA/SAC/DSV/DRM/NeuroSpin
> Bât 145, Point Courrier 156
> F-91191 Gif/Yvette, FRANCE
> Tel : +33 1 69 08 99 74
> Fax : +33 1 69 08 79 73
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
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