# Visualization of MRI data in R

Lately I was getting a little bored with genomic data (and then TCGA2STAT started to give me a segfault on my university’s high performance computing facility too ). So I decided to analyze some brain imaging data that I had lying around instead. The first step is to do some visual data exploration. In this blog post I present some functions which I was able to find for MRI visualization in R, and which I found to be very useful. All functions presented below presuppose an image in the NIfTI data format as input, and are very user-friendly.

# Turn an old laptop into a home server with remote access over VPN

This weekend I have set up an old laptop with a broken screen as an Amahi server in my house, such that I can access the files stored on the server with my other computers from anywhere.1 I use OpenVPN to establish a connection to the server and its files. As an additional benefit, connecting over a VPN when on a public network secures the traffic to and from you.

1. Initially I got the idea for a home server after an email from Dropbox informed me that my promotional 48 GB of storage space expire in a month. Instead of paying one of the numerous cloud storage providers, I decided to host an ownCloud at home (after some guides online made it sound easier than it actually is…). Unfortunately, ownCloud on an Amahi server turned out to be quite disappointing. I found ownCloud to lack some functionality and to be very inconvenient in certain ways, and it possibly poses a security risk when accessible from outside the local network. So, I eventually got rid of ownCloud, and retreated to storing my files directly on the server in file shares

# Generalized inverse of a symmetric matrix

I have always found the common definition of the generalized inverse of a matrix quite unsatisfactory, because it is usually defined by a mere property, $A A^{-} A = A$, which does not really give intuition on when such a matrix exists or on how it can be constructed, etc… But recently, I came across a much more satisfactory definition for the case of symmetric (or more general, normal) matrices.

# Logistic regression with categorical data in Ruby

I had some fun analysing the shelter animal data from kaggle using the Ruby gems daru for data wrangling and statsample-glm for model fitting. In this blog post, I want to demonstrate that data wrangling and statistical modeling is not an area of absolute predominance of Python and R, but that it is possible in Ruby too (though, currently to a much lesser extent).

# My first R package on CRAN

A couple of weeks ago I have released my first R package on CRAN. For me it turned out to be a far less painful process than many people on the internet portray it to be (even though the package uses quite a lot of C++ code via Rcpp and RcppEigen, and even though R CMD check returns two NOTEs). Some of the most helpful resources for publishing the package were:

# "Testing Statistical Hypotheses" and "Theory of Point Estimation" impressions

I spent much of the last two months reading Lehmann & Romano “Testing Statistical Hypotheses” (3rd ed.) and Lehmann & Casella “Theory of Point Estimation” (2nd ed.), abbr. TSH and TPE. The following is a collection of random facts observations I made while reading TSH and TPE. The choice of topics is biased towards application in regression models.