myGuide Blog

DTI analysis: An outline

DTI analysis: An outline

An outline of DTI dataset processing pipeline for TBSS analysis as well as probabilistic tractography using FSL. DTI data processing Data preparation Convert dicom files to nifti Use dcm2nii or dcm2niigui from mricron Rename...

Real-time functional MRI related papers

Real-time functional MRI related papers

Real-time functional MRI is one of my research interests. So from today, I will start compiling a list of papers related to the topic. I will list the paper here after reading it. This...

VIM commands

VIM commands

Quick VIM commands for common editing tasks Search and replace :s/foo/bar/g – change ‘foo’ to ‘bar’ in the current line :%s/foo/bar/g – change ‘foo’ to ‘bar’ in all lines Cut and paste position cursor...

Generate your own “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...

Time series-based bifurcation analysis

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....

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

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...

Looking at how the brain works in real-time

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...

When the virtual world merges with the real one

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...

Creating a backup SVN repository

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 remote.com...

Correlation coefficient

Correlation coefficient

Definition 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.

Connect to Server

Accessing Windows share in Linux

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...

Matlab scripting quick tip: Dual monitor setup

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...

Installing Youtube Direct

Installing Youtube Direct

Youtube Direct is a new tool from Google/Youtube that makes it easier for media organizations or websites to request users to submit video clips, review submitted clips, and possibly re-broadcast these clips, just like...

NinfG and Firewall

NinfG and Firewall

The latest version of NinfG (version 5.0) has a lot to offer in terms of allowing client-server connectivity. First, it introduces the invoke server module separating components used to invoke remote applications from the...

How to change hostname in Linux

How to change hostname in Linux

In order to change the hostname of your linux machine, you can do the following: 1) Edit file /etc/sysconfig/network using your favourite editor, say using vi. 2) Look for the line with HOSTNAME in...

Debugging with gdb

Debugging with gdb

GDB is the GNU project debugger which can be very helpful when you’re trying to figure out what goes wrong in the application you’re developing. With gdb, you can start a program, specify points...

All about SVN

All about SVN

Subversion (or SVN) is an open source version control system that can be used to maintain several versions of files such as program source codes, webpages, and other documentation. It has several features including...