How to get a graph for each subject

[Hui Xu]

Hi Chris,

I am now using brainGraph (Version 3.0.0) to do the structural covariances networks. The cortical thickness was obtained from recon by using freesurfer. Based on chapter 6 of the user guide (Version 3.0.0), I can't get each graph for each subject. How can I get a graph for each subject for later analysis (such as vertex-wise group analysis) ?

Best,

Hui

[Hui Xu]

Hi Chris,

More detailed information are listed below:

In Chapter 8, on page 50 (brainGraph User Guide Version 3.0.0),

"Analysis of between-group differences in a given vertex measure (e.g., degree, betweenness centrality, etc.) is described in this chapter (equivalent to a voxel-wise analysis common in fMRI, DTI, VBM, etc. analyses). This is only possible if you have a graph for each subject (at a given density/threshold)." This mean if I wanna do the analysis of between groups, I need to have a graph for each subject.

However, based on Chapter 6, I ran the following code, and I can't get a graph for each subject, can you help me to figure out how this happened?

" g.subject <- lapply(seq_along(densities), function(x)
        make_brainGraphList(corrs[x], atlas='dk',
                            level = "subject",
                            weighted=TRUE,
                            modality='thickness', .progress=F)) "

Many thanks!

Hui

[Chris Watson]

You will have to create individual subject-level data using some other software. With Freesurfer's outputs, you can only do group-level graphs. For group analysis, you will have to use permutation testing which is described later in the User Guide; see Chapters 12 and 13.

Chris

[Hui Xu]

Hi Chirs,

Thank you so much for your reply. It's my first time using brainGraph to perform structural networks. Can you recommend some other softwares which can create individual subject-level data?

Another question is that in Chapter 8, what is the input for group analysis in your example? Is it not from Freesurfer's outputs?

Hope in your next update about the user guide, you can use the open source data to do all analyses, which will make freshmen like me learn this amazing toolbox quickly. In that way, we can use the data and code together.

Best,

Hui

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