Newbie getting started with brainGraph

[E Ji]

Dear Chris and experts,

I am using brainGraph for the first time and also familiarizing myself with R. I've read through the User Guide and now trying to make sure I start off correctly. I have a few questions.

- The brain rois we are using are from a custom atlas containing 318 regions. Aside from setting atlas=’custom’ at some point, how should I format the custom atlas / feed it in? (see attached custom_atlas.csv)

- Our correlation matrices have already been binarized using a sparsity threshold prior to using brainGraph. Is it possible to use the binarized matrices as a starting point rather than the correlation matrix? (see attached binarized_matrices.csv)

- In order to calculate our indices of interest, do these steps seem logical?

1. make_brainGraph

2. make_brainGraphList

(what is the difference between these two first steps?)

3. set_brainGraph_attr in order to calculate our metrics of interest

4. plot_brainGraph_gui to visualize

Finally, I believe the 3 attachments are the only relevant input needed to get started. Basically, we have n=438 subjects but I've cut it down to n=3 here to keep things simple for now.  It would be great if you could confirm whether things appear to be set up correctly.

Thank you for helping me to get started!

Best,

EJ

[Chris Watson]

I apologize for such a long delay. I started a new position and a few new projects, and have been working on proposals/submissions. I hope it has not delayed you too much in learning R and network analysis.

Your atlas data table will need columns for, in addition to region names, MNI coordinates, hemisphere, lobe (if possible), and index (which just goes from 1 to 318 in your case). See Chapter 1.5 of the User Guide.

The region names of your networks will have to match the names in the atlas (not region_XX). You will also have to reorder your data since it is in one large table. This may be tricky and I do not know right away the best way you can do this. They should be in a 3D array, ideally.

Then if you're creating "brainGraphList" objects, you wouldn't use "make_brainGraph" directly (as it gets called from "make_brainGraphList").

Chris

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