Generate your own “research wordle”

my research wordle

Wordle is an online app for generating “word clouds”, a kind of visual representation for text data. It gives greater prominence to words (e.g., by  using larger font size or different font color) that appear more frequently in the provided text source or in the text of a given URL. SciVerse has a new app called “Author Wordle” that creates a wordle word cloud based on the titles of the last 100 publications of any author that can be found in Scopus.

Time series-based bifurcation analysis

Re-posting this one from my old university website. A brief introduction of my graduate research topic.

Studies in nonlinear time series analysis have provided reliable techniques for the evaluation of signals from dynamical systems. Some of these techniques are used to gain insights into the unknown physical processes, to do prediction, as well as to determine invariants associated to the dynamics of the system. Others are employed to determine whether irregularities in signals are due to the intrinsic nonlinearity of the system or are caused by extrinsic random processes impinging on the system. Several others are applied to build models capturing the dynamics of the system from the observed data. In this study, new methods to uncover the underlying mechanisms of dynamical systems using time series are introduced. This set of algorithms can be used to evaluate how sensitive the system is to the values of its parameters and how the system’s behavior changes as the parameters are varied. Since these issues are best explored by means of bifurcation diagrams (BDs), this work describes the algorithms in constructing BDs from time series.

Splitting 4D Nifti file into a series of 3D files in Matlab

NIfTI-1 is a data format proposed by the NifTI (Neuroimaging Informatics Technology Initiative) DFWG (Data Format Working Group) that can be used for storing neuroimaging datasets (e.g. MRI, functional MRI, etc.). This format is adapted from the widely used ANALYZE 7.5 format from Mayo Clinic. A Nifti file consists of a header part containing the meta-data and the raw image data itself. The header and the image data can be stored together in the same file with an *.nii extension or can be split into two files with an *.hdr extension for the header and an *.img extension for the image data.

Looking at how the brain works in real-time

Activation Maps

Re-posting this article on real-time functional MRI I wrote several years ago.

The technique known as functional magnetic resonance imaging (fMRI) has been extensively used to elucidate the functions of the human brain. Functional MRI provides a “window” where we can see what part of the brain is involved when we think, smell, taste, feel, or move. These windows are the activation maps indicating sites in the subject’s brain that are activated while the subject performs a given task and are usually obtained after analyzing voluminous amount of functional MRI images.

When the virtual world merges with the real one

Just want to share this YouTube video from MicrosoftResearch. It’s just amazing. The idea is to augment the real environment with a virtual one and interact with it. Using four ceiling-mounted Kinects, the entire room is mapped into a virtual 3D environment. Virtual objects can be placed in this virtual environment and projected into the real one using handheld projectors. The interaction is quite impressive.

Creating a backup SVN repository

This is a brief guide on how to setup a backup SVN repository using svnsync. I will assume that subversion is already installed and the master repository is located in the machine called and in the directory /home/ruser/master_repos directory.

Correlation coefficient



Given two random variables X and Y, Pearson’s correlation coefficient ρ is defined as the ratio between the covariance of the two variables and the product of their standard deviations:

Of vector and matrix products


Listed below are definitions of some vector or matrix products. I will be needing these definitions in the succeeding posts. Thanks to Jetpack‘s Latex support, I can now include equations in my post.

Accessing Windows share in Linux

Connect to Server

There are several ways to do this. One is GUI-based. In Fedora Core, use the Places menu in the top panel. Within this menu item, click the ‘Connect to Server…’ sub-menu. This will popup the Connect to Server dialog box shown below.

Matlab scripting quick tip: Dual monitor setup

I have been using Matlab for almost all of my computing needs. It is very easy to program especially when dealing with matrices. It has also a rich library of graphical interface. You can easily build a highly interactive graphical user interface using its GUI development environment or GUIDE. If you are familiar with event-based programming, you will have no difficulty using GUIDE.

Here is a quick tip you might find useful when programming in Matlab.