Thanks
Best
Maedeh
-----Original Message-----
From: Soroosh Afyouni <[log in to unmask]>
To: [log in to unmask]
Date: Sat, 22 Dec 2018 22:52:28 +0000
Subject: Re: [FSL] A General Question about Graph Analysis
> Also BCT:
> https://sites.google.com/site/bctnet/
> might be of help.
>
> -Soroosh
>
> On Sat, 22 Dec 2018 at 20:51, Maedeh Khalilian
> <[log in to unmask]>
> wrote:
>
> > Dear Tim
> > Thanks a lot for your suggestions and explanation. My file formats
> are
> > ".mat" and ".csv" which are made by different softwares. And my
> graphs are
> > not that much large.( at most 1k nodes). I will definietely check
> them.
> > Thanks more.
> > Maedeh.
> > -----Original Message-----
> > From: Tim Schäfer <[log in to unmask]>
> > To: [log in to unmask]
> > Date: Sat, 22 Dec 2018 20:59:32 +0100
> > Subject: Re: [FSL] A General Question about Graph Analysis
> >
> > > Regarding experiences: They are both general graph analysis tools,
> not
> > > specific to neuro science. I don't know in which graph file format
> you
> > > have that graph, but they both read tons of standard graph file
> > > formats, and you should be able to export in one of these formats.
> > > (Some formats are so simple that you can write your own exporter
> in a
> > > few lines of Matlab - or whatever - code.)
> > >
> > >
> > > I've used both Gephi and Cytoscape to compute and visualize graph
> > > metrics for a various biological networks, including some pretty
> large
> > > graphs representing atom connectivity in proteins. Visualization
> gets
> > > slow if you have several 10k nodes, but that should not happen in
> your
> > > case I guess.
> > >
> > > I should also add that I used both tools in a different field, I
> have
> > > no idea whether they are commonly used in neuro science.
> > >
> > > Tim
> > >
> > >
> > > > On December 22, 2018 at 6:42 PM Maedeh Khalilian
> > > <[log in to unmask]> wrote:
> > > >
> > > >
> > > > Dear experts and users,
> > > > I have a general question, actually not sure if it is proper to
> ask
> > > here or
> > > > not!
> > > > I have a connectivity matrix, I am looking for an efficient and
> > > convenient
> > > > toolbox or software that can calculate the parameters of the
> graph
> > > such as
> > > > clustering coefficient, path length ,etc for me.
> > > > I would be grateful if u could share your experiences and
> suggestions
> > > with
> > > > me.
> > > > Best regards,
> > > > Maedeh,
> > > >
> > > >
> > >
> #######################################################################
> > > #
> > > >
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> > >
> > > --
> > > Dr. Tim Schäfer
> > > Postdoc Computational Neuroimaging
> > > Department of Child and Adolescent Psychiatry, Psychosomatics and
> > > Psychotherapy
> > > University Hospital Frankfurt, Goethe University Frankfurt am Main,
> > > Germany
> > >
> > >
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> >
> >
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> --
> -Soroosh
>
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