Archive for the ‘XNAT’ Category

Clojure and XNAT: Introduction

Saturday, February 4th, 2012

Clojure and XNAT: Introduction

Over the last two years, I’ve been using Clojure quite a bit for managing, testing, and exploratory development in XNAT. Clojure is a new member of the Lisp family of languages that runs in the Java Virtual Machine. Two features of Clojure that I’ve found particularly useful are seamless Java interoperability and good support for interactive development.

“Interactive development” is a term that may need some explanation: With many languages — Java, C, and C++ come to mind — you write your code, compile it, and then run your program to test. Most Lisps, including Clojure, have a different model: you start the environment, write some code, test a function, make changes, and rerun your test with the new code. Any state necessary for the test stays in memory, so each write/compile/test iteration is fast. Developing in Clojure feels a lot like running an interpreted environment like Matlab, Mathematica, or R, but Clojure is a general-purpose language that compiles to JVM bytecode, with performance comparable to plain old Java.

One problem that comes up again and again on the XNAT discussion group and in our local XNAT support is that received DICOM files land in the unassigned prearchive rather than the intended project. Usually when this happens, there’s a custom rule for project identification where the regular expression doesn’t quite match what’s in the DICOM headers. Regular expressions are a wonderfully concise way of representing text patterns, but this sentence is equally true if you replace “wonderfully concise” with “maddeningly cryptic.”

Interesting “introduction” that focuses on regular expressions.

If you don’t know XNAT (I didn’t):

XNAT is an open source imaging informatics platform, developed by the Neuroinformatics Research Group at Washington University. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data. Thanks to its extensibility, XNAT can be used to support a wide range of imaging-based projects.

Important neuroinformatics project based at Washington University, which has a history of very successful public technology projects.

Never hurts to learn more about any informatics project, particularly one in the medical sciences. With an introduction to Clojure as well, what more could you want?