Compute pairwise correlations from fMRI data in Matlab
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README.md

corr-m

Matlab tools for computing pairwise correlations from fMRI data

Facilitates fast correlation computation for pairwise internodal functional connectivity estimation based on fMRI data. So far, two measures of association are supported: Pearson's r and the tetrachoric correlation coefficient. With Pearson's r, efficient implementation (based on CPU instruction set extensions) and parallelization yield speedups up to ~3x compared to Matlab's corrcoef (R2011b). With the tetrachoric correlation coefficient, data reduction in the temporal domain based on binarization of nodal time series combined with tetrachoric correlation estimation and efficient implementation (based on a 16-bit lookup table or CPU instruction set extensions) and parallelization yield speedups up to ~20x compared to Matlab's corrcoef (R2011b).

Prerequisites
  • 64-bit Linux
  • 64-bit Matlab
  • The GCC C compiler
  • A working MEX setup that uses GCC to compile the MEX files
Download

Obtain an archive containing the lastest version from http://www.kristianloewe.com or clone the repository using

$ git clone --recursive https://github.com/kloewe/corr-m.git
Installation

Change to the root directory of the extracted archive (or the cloned repository) and install corr-m and cpuinfo-m.

$ ./install-m.sh corr-m <target-dir-corr-m>
$ ./install-m.sh cpuinfo-m <target-dir-cpuinfo-m>

It is assumed here that Matlab is on your path and that MEX is set up.

Next, start Matlab and add the relevant directories to its path.

>> addpath <target-dir-corr-m>
>> addpath <target-dir-cpuinfo-m>
Documentation

A description of each function can be displayed in Matlab using

>> help <function-name>
Bugs

If you run into problems, please send an email to kl@kristianloewe.com.

Citation

If you use this program, please cite:

Loewe K, Grueschow M, Stoppel C, Kruse R, and Borgelt C (2014).
Fast construction of voxel-level functional connectivity graphs.
BMC Neuroscience 15:78.
doi