The following may be of interest to users. I will organise a Thursday evening ynic seminar in the new year to discuss its use and alternative packages Gary -------- Forwarded Message -------- Subject: FW: Graph theory analysis in R Date: Mon, 14 Dec 2015 19:01:40 +0000 From: Watson, Christopher <Christopher.Watson(a)CHILDRENS.HARVARD.EDU> Reply-To: FSL - FMRIB's Software Library <FSL(a)JISCMAIL.AC.UK> To: FSL(a)JISCMAIL.AC.UK Dear FSL users, (apologies for cross-post) I am pleased to announce the release of an R package I created, called "brainGraph", for performing graph theory analyses of brain MRI data. You can use it for cortical thickness, volume, surface area, or LGI. It can also be used for tractography data (I have code that works with the outputs of FSL's "probtrackx2"), and it should work for resting-state fMRI as well. It is very heavily dependent on the fantastic R package "igraph" (see http://igraph.org/redirect.html). I created a GUI for quick and easy data exploration, but it isn't quite as polished as others out there (e.g., BrainNet Viewer). For usage, please see the User Guide I put together (direct PDF link: https://www.dropbox.com/s/j831n3q9muyz1go/brainGraph_UserGuide.pdf?dl=0 ). You will find some code for getting your data into R, and I have documented many analysis steps and include multiple figures. I hope this is intuitive for both veteran and novice R users. Additionally, there are System Requirements, Installation instructions, and links for help learning R. Some features that should be of interest include: * bootstrapping & permutation testing * random graph generation, small-worldness, and global/local/nodal efficiency * rich-club calculations * robustness ("targeted attack" or "random failure") & vulnerability: PDF of figure (PNG: https://www.dropbox.com/s/k14gdg1lomhh4l2/failPlot-1.pdf?dl=0) * Plotting GUI - full GUI (PNG): https://www.dropbox.com/s/e0hdng7flrxsgd2/brainGraph_GUI.png?dl=0 * Plotting GUI - union of vertex neighborhoods (PNG): https://www.dropbox.com/s/aag5cn1p1z9xzxr/brainGraph_GUI_neighborhoods.png?… * Plotting GUI - community (module) plots (PNG): https://www.dropbox.com/s/8zzpd5j268qstmg/brainGraph_GUI_communities.png?dl… You can install it directly in R by typing: install.packages('brainGraph') My Github page for the package (https://github.com/cwatson/brainGraph) contains the development version, and you can install that by typing: devtools::install_github('cwatson/brainGraph') Please see the NEWS.md file (https://github.com/cwatson/brainGraph/blob/master/NEWS.md) for updates made since the CRAN submission. To work properly on Windows, you may need to install the devel version. This is still a work-in-progress, so I am very happy to receive bug reports, feature requests, general coding help questions, (constructive) criticism, etc. Please join the Google Group that I set up for those purposes: https://groups.google.com/forum/?hl=en#!forum/brainGraph-help Chris Watson