[FieldTrip] Error with mutual information

[Gian Marco Duma]

In the ft_connectivity_mutualinformation the indication of the data input
is 'The input data should be a Nchan x Nobservations matrix'. My data is a
classic n-ny-m matlab matrix with the n= number of channels (in my case the
vertices of the source) and m= number of time points. I thought that maybe
reducing the source vertices (by downsampling to an atlas) could help, but
it is not the dimension of my matrix the problem, since I continue to have
the same error.
That's why I'm not sure where the error comes from.
best
Gian Marco

Il giorno gio 18 feb 2021 alle ore 15:15 Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> ha scritto:

> Ciao Gianmarco,
>
> I guess the answer on your question ‘what am I doing wrong’ depends on how
> you have formatted your Brainstorm-derived data into a structure that
> fieldtrip can work with.
> If you are working with ft_connectivity_mutualinformation directly, you
> should study a bit what the required formatting of the input matrix is.
> Probably the order of the dimensions or the orientation of the matrix is
> wrong.
>
> Best wishes,
> Jan-Mathijs
>
>
>
> On 18 Feb 2021, at 10:57, Gian Marco Duma <gianmarco.duma at unipd.it> wrote:
>
> Xavier, thanks for your quick reply. I solved the installation problem,
> however I have two more questions. I'm not sure how to compute mutual
> information with the ft_connectivityanalysis function, since I did not find
> mutual information within the methods section of the function.
> The second question is: my data are basically  resting state source
> activity I extracted from brainstorm with the dimensions 15002 (vertices) x
> 2000 (time). In the mutualinformation function says 'The input data should
> be a Nchan x Nobservations matrix'. However, when I try tu
> run ft_connectivity_mutualinformation I receive the following error:
>
> Error using entropy
> Too many input arguments.
>
> Error in information (line 501)
>   [H{:}] = entropy(R, opts, outputOptsList{:});
>
> Error in ft_connectivity_mutualinformation (line 156)
>           output(k,p,m) = information(R2, opts, 'I'); % this computes
> mutual information
>
> What am I doing wrong?
> Thanks
>
> Il giorno gio 18 feb 2021 alle ore 03:13 Xavier Vrijdag <
> x.vrijdag at auckland.ac.nz> ha scritto:
>
>> HI Gian,
>>
>>
>>
>> I am using the mutual information analysis provided by the IBTB toolbox
>> in fieldtrip.
>>
>>
>>
>> You can check in the fieldtrip/external/ folder if the IBTB folder
>> exists. In my fieldtrip downloads the IBTB toolbox is available. Otherwise
>> you can download it from the fieldtrip github:
>> https://github.com/fieldtrip/fieldtrip/tree/master/external/ibtb
>>
>>
>>
>> In general, I can recommend you to use the ft_connectivityanalysis
>> function instead of the lower-level function
>> ft_connectivity_mutualinformation.
>>
>>
>>
>> Regards,
>>
>>
>>
>> Xavier
>>
>>
>>
>> *From: *fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Gian
>> Marco Duma <gianmarco.duma at unipd.it>
>> *Reply to: *FieldTrip discussion list <fieldtrip at science.ru.nl>
>> *Date: *Thursday, 18 February 2021 at 12:14 PM
>> *To: *"fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
>> *Subject: *[FieldTrip] Error with mutual information
>>
>>
>>
>> Hi everyone, I'm trying to run mutual information as a measure of
>> functional connectivity. When I run the
>> command  ft_connectivity_mutualinformation I receive the following message
>>
>>
>>
>> Error using ft_hastoolbox (line 450)
>> the IBTB toolbox is not installed, see http://www.ibtb.org
>>
>> Error in ft_connectivity_mutualinformation (line 48)
>> ft_hastoolbox('ibtb', 1);
>>
>>
>>
>> The web site reported in the error line is not active anymore.
>> Therefore I downloaded the ibtb toolbox from the supplementary material of
>> the paper Magri et al. 2009, at the following link
>>
>> https://link.springer.com/article/10.1186/1471-2202-10-81
>>
>>
>>
>> I installed as usual the toolbox, I decompressed it and I added it to the
>> matlab path as suggested by the installation file. However I continue to
>> receive the same error message.
>>
>> Do you have any suggestions?
>>
>> Thanks
>>
>>
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>> https://doi.org/10.1371/journal.pcbi.1002202
>>
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