As the first Ph.D. through a young lab I spent a lot of time learning new analytical tools and developing beginner level manuals to transfer that knowledge to the next generation of students. This page archives some of these statistical and brain imaging manuals intended for novices.

R for beginners

R is an open source statistical package that permits an incredible degree of control and transparency in statistical analyses. However, doing stats from the command line is a double edged sword. On one hand, R gives you unparalleled freedom to explore and analyze your data. On the other hand, getting a handle of the basic commands can be daunting for new users and analyses that would have been but a matter of a few clicks in other statistical packages can seem like arduous work.

This workshop is a series of four R scripts  that can be run line by line as a demonstration of some of the basic functionality of R. These were originally meant to be accompanied by verbal guidance, but they are also heavily annotated so a well motivated student should still find them useful. At the very least, the scripts provide a healthy stock of sample code from which to explore.

MRI analysis guides

Human brain imaging demands an incredible amount of theoretical knowledge  spread across disparate disciplines including neurobiology, physics, software programming and statistics, not to mention the arcana of operating individual software packages. To ease the burden on new students I’ve assembled some simple guides for a few common software packages for MRI data analysis.

functional MRI

BrainVoyager is pretty intuitive for someone who’s just starting out, but it has some pretty serious limitations that make it impractical for experts. Here is a simple but thorough guide to BrainVoyager for anyone who is just learning how to analyze MRI data (if they can afford its prohibitively expensive price tag), but keep in mind that you may eventually want to migrate elsewhere.

FSL looks a little clunkier but it’s free, has fewer limitations, and is particularly easy to batch process. This FSL guide covers simple fMRI analyses.

SPM is also free and flexible (assuming that you have a MATLAB license). I find the GUI a little cumbersome for processing anything more than single participants, but scripting your processing pipeline is fairly intuitive. Here are guides for the SPM GUI and  SPM command line, as well as some sample code.

Diffusion tensor imaging

Tract Based Spatial Statistics (TBSS) as implemented in FSL is a method for testing hypotheses related to white matter tract integrity as measured by fractional anisotropy. This TBSS guide is a step by step manual for analyses diffusion tensor data.


Activation Likelihood Estimation (ALE) is the current standard approach for analyses of fMRI data. ALEs can be computed using GingerALE software relatively easily, but here are guides for both the GUI and Command line.

ALE is an excellent tool, but it does make some strong assumptions about the studies that you analyze. One assumption in particular is frequently violated. All of the studies in your analysis should have scanned the entire brain volume. This can be problematic for meta-analyses from a smaller literature, literature’s where full brain coverage is uncommon, or for research questions that only really need to test hypotheses for a single brain area. My alternative solution is to use Kernel Density Estimation. You can find a description of this approach, tests on simulated data, and some sample code with this paper.

TMS Neuronaviagtion guides

Transcranial magnetic stimulation is a tool for brain stimulation that has applications for  scientific discovery and is starting to find it’s way into the clinic. While there are some low-tech solutions for guiding TMS stimulators to their target locations they risk being wildly inaccurate and make the spatial specificity of TMS more of a liability than an asset. Neuronavigation technologies combine anatomical MRIs with motion tracking for precision neural targeting. Here’s my guide to Brainsight‘s neuronavigation system.