Intro to myself and my project

 

It’s really excited to get accepted into Google Summer of Code project. I will make contribution to DIPY (Diffusion MRI analysis) in Python. I’m a master student in computer science at Indiana University. Right now, I’m trying to merge my interest in both medical physics and computer science, more specifically to apply machine learning and other technology of computing to medical imaging and radiotherapy. So I think this project will be good experience for me.

My project is to implement multi-thread capacities for nonrigid registration in DIPY using OpenMP. In DIPY, it implements a broad range of algorithms for denoising, registration, reconstruction, fiber tracking, clustering, visualization, and statistical analysis of MRI data. For nonrigid image registration, the major goal is to calculate a deffeomorphic transformation to register two 2D images or 3D volumes. To achieve this, we need to do a lot of iterations to maximize the similarity metric, thus it slow down the optimization process.

To speed up the calculation, one solution is to convert to a parallel computing algorithm. The OpenMP API supports multi-platform shared-memory parallel programming in C/C++ and Fortran. Due to Global Interpreter Lock (GIL), there is no point to use threads for CPU intensive tasks in Python. Fortunately, with the help of Cython, we can release GIL during computations. So in this project, I will implement a multi-thread parallel algorithm using OpenMP and Cython to improve the performance of nonrigid image registration in DIPY.

It’s amazing that I just started to learn how to code in Python, and right now I have made some contributions to the open source software of DIPY in Python. See my pull requests┬ábefore applying for this project. Also It’s really lucky for me to get my name (Ricci Woo) added into the contributors of DIPY release 0.14. In this bonding period, I learned basic principle in Diffusion MRI and image processing. Also I learned how to profile runtime of functions in Python to see which function is the most expensive one, then I can work on improving performance on it.

Oh, I forgot to tell my name. That is Xinquan Wu (Legal), or you can call me Ricci Woo (Nickname). You can contact me at email: ricciwoo@gmail.com. I will push my code to my fork of DIPY on GitHub.

Leave a Reply

Your email address will not be published. Required fields are marked *