brain

Convert images to matrix

Quite often you need to convert an image (or multiple images) to a MatLab matrix for further analysis and visualization (e.g. extracting time series, multivariate pattern analysis, etc). SPM provides handy functions for this: P = spm_select; % select
Xu Cui
21 sec read

Wavelet Coherence

Wavelet transform coherence (WTC) is a method for analyzing the coherence and phase lag between two time series as a function of both time and frequency (Chang and Glover 2010). Here I played with it using the MatLab toolbox provided by Grinsted et a
Xu Cui
1 min read

Standard deviation and standard error

Standard deviation (std): standard deviation of the sample Standard error, or standard error of the mean (sem), is the standard deviation of the mean. \(sem=std/\sqrt{N}\) Most errorbars in scientific publications refer to standard error. Quite often
Xu Cui
22 sec read

Meaning of correlation coefficient

If variable X and Y has correlation 0.1, how much does it help to predict Y based on X? In the simplest binary case, the probability (p) to correctly predict Y based on X is a linear function of correlation (c), i.e. $$p=\frac{c+1}{2}$$ That means, a
Xu Cui
14 sec read

How to determine the voxel size in an image

Tools: SPM, cor2mni Assume the image is “a.img”, do v = spm_vol('a.img'); v.mat If v.mat is a diagonal matrix, you can simply read the number and they are the voxel size in mm. If not, a trick is to calculate the distance between adjacent
Xu Cui
40 sec read

SVM regression with libsvm

SVM is mostly commonly used for binary classifications. But one branch of SVM, SVM regression or SVR, is able to fit a continuous function to data. This is particularly useful when the predicted variable is continuous. Here I tried some very simple c
Xu Cui
1 min read

Brain surface plot with MatLab

This is an example of brain activation plotted on surface. In many circumstances surface view is much more straightforward than a slice view. Here is how I created such a plot using MatLab and SPM. Environment and Tools: Windows XP MatLab (v7.6) SPM
Xu Cui
1 min read

tcpip connection with pnet

We use TCP/UDP/IP Toolbox 2.0.5 to read and write data from/to a TCPIP port. It’s fast and reliable. The version we use is 2.0.5. Below is a matlab sample script showing how to connect to another computer (called ETG-4000) with TCPIP : %Connect
Xu Cui
1 min read

Noise removal in NIRS

Noise removal methods in NIRS can be divided into 4 categories: reducing noise based on its temporal characteristics: The instrument noise is usually in the high frequency band and thus can be removed by band pass filtering. Band pass filtering can a
Xu Cui
41 sec read