Error extracting graph theory measures - brain connectivity toolbox

Dear experts,

I have a 90x90 connectivity matrix and am trying to extract graph theory measures using the brain connectivity toolbox, in particular the characteristic path length.I used the following code

load('01_DWI_FP_MD_C_trafo_Tracts_CSD_FA_PASS' )

>> charpath(CM)

But then I get the following error message "Error using charpath. The distance matrix must not contain NaN values"

I checked and indeed there are several NaN values in the matrix - can anyone provide suggestion on how to sort this error? Should the NaN be replaced by real values and if so how to do this? 0 or 1 values? I also attach the connectivity matrix

Sorry but I am very new to programming and any suggesting would be welcomed.

Thanks in advance,

Jose

[Walter Roberson]

NaN cannot be a connection, so you would replace the NaN with 0.

[Jose Teles]

Thank you for the reply.

Is there any script/code I could use to perfom this change from NaN to zero?

[Walter Roberson]

CM(isnan(CM)) = 0;

[Jose]

Dear Walter,

Thank you very much again for your reply. The script you suggested did changed the NaNs to zero however when I call again the function charpath(CM) I got a new error message:

"Undefined function 'nanmax' for input arguments of type 'double'.

Error in charpath (line 72)

ecc = nanmax(D,[],2);"

I really don´t know why this error appears perhaps you could provide some suggestion?

Thank you

[Walter Roberson]

nanmax() is part of the Statistics toolbox; https://www.mathworks.com/help/stats/nanmax.html

You can instead use

ecc = max(D, [], 2);

Or for greater readability of intent,

ecc = max(D, [], 2, 'omitnan');

omitnan is the default.

[Jose]

Thank you for suggestion, I called the function upon but still there is the error "Unrecognized function or variable 'D'"

"ecc = max(D, [], 2, 'omitnan');

Unrecognized function or variable 'D'"

Can you help?

[Walter Roberson]

Is charpath() your function or one from the Brain Function Toolbox? If it is your function we would need to see the code; if it is from the toolbox we will need a link to the toolbox.

[Jose]

Hello Walter,

The toolbox I am using is the brain connectivity toolbox (https://sites.google.com/site/bctnet/)

The function I want to run from the toolbox is the characteristic path length – charpath (https://sites.google.com/site/bctnet/list-of-measures)

I also attach the matlab function of the measure perhaps this helps?

I am stuck not sure why I am getting these errors.

Thank you

[Walter Roberson]

It is not possible to reach that line of code without having executed

n = size(D,1);

which would have complained if D was not passed in to the function.

Please go back and re-run the charpath(CM) call ... after, that is, having changed the line

ecc        = nanmax(D,[],2);

at line 72, to be

ecc        = max(D,[],2,'omitnan');

and saving the charpath.m file.

[Jose]

Thank you Walter for your help this worked