[FieldTrip] Error with mutual information

[Schoffelen, J.M. (Jan Mathijs)]

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<mailto: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<mailto: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<mailto:fieldtrip-bounces at science.ru.nl>> on behalf of Gian Marco Duma <gianmarco.duma at unipd.it<mailto:gianmarco.duma at unipd.it>>
Reply to: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Date: Thursday, 18 February 2021 at 12:14 PM
To: "fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>" <fieldtrip at science.ru.nl<mailto: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<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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