conan documentation

conan is a toolbox for functional CONnectivity ANalysis in Matlab.

Installation

Prerequisites

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

Download

Clone the repository.

$ git clone --recursive https://github.com/kloewe/conan.git

Build

Change to the root directory of the cloned repository and build the MEX files.

$ cd conan
$ make

Set up

Add the relevant directories to Matlab’s search path and save it.

$ make install

Alternatively, you can manually add the relevant directories to Matlab’s search path and optionally save it.

>> addpath('<conan-dir>/mod/corr-m')
>> addpath('<conan-dir>/mod/cpuinfo-m')
>> addpath('<conan-dir>/mod/fconn-m')
>> addpath('<conan-dir>/mod/util-m')
>> savepath

Matlab Functions

Usage

A description of each function can be displayed in Matlab using

>> help <function-name>

Functions

Pairwise correlations (corr-m)

Function Synopsis
pcc Compute pairwise Pearson correlation coefficients.
sub2utm Linear index (wrt upper triangle) from matrix subscripts.
tetracc Compute pairwise tetrachoric correlation coefficients.
toSymMat Convert vector of upper triangular elems into a symmetric matrix.

Processor information queries (cpuinfo-m)

Function Synopsis
corecnt Determine the number of processor cores.
cpuinfo Determine availability of instruction set extensions on the CPU.
proccnt Determine the number of logical processors.

Functional connectivity (fconn-m)

Function Synopsis
fcmNodeMetrics Nodal metrics of functional connectomes.
mfcmStats Element-wise statistics across multiple functional connectomes.
volClust Volume clustering and cluster properties.
volClustPermTest FWE-corrected cluster-level p values based on permutations.

Utilities (util-m)

Function Synopsis
circos  
  genCircosConf Generate a Circos configuration.
  rgb2colordef Create color definitions file for use with Circos.
data  
  clipData Clip/winsorize data according to the specified clipping limits.
  cutData Cut data according to the specified limits.
  flat Flatten an array of data.
  rescaleData Rescale (linearly transform) data to the specified range.
file  
  fileCountLines Count the number of lines in a file.
  fileExists Check if a given file exists.
  fileGetDir Get directory from full path.
  fileGetExt Get extension from full path.
  fileGetName Get filename from full path.
  fileGlob Filename expansion.
mri  
  readImgData Read neuroimaging data.
  readImgHdr Read header information for neuroimaging data.
  writeImgData Write neuroimaging data to a NIFTI file.
perf  
  getPageSize Get page size using getconf.
  monMem Monitor memory usage using the proc filesystem.
  monPerf Monitor performance based on event counters using perf stat.
plot  
  blend Composite image A over image B.
  pngcolorbar Save a colorbar in png format.
pool  
  poolmgr Unified parallel pool management across Matlab versions.
ui  
  drawOutline Draw 2D outline.
  getAxesBelowPointer Get axes below the mouse pointer.

References

If you use conan, please cite:

Loewe K, Donohue SE, Schoenfeld MA, Kruse R, Borgelt C (2016).
Memory-efficient analysis of dense functional connectomes.
Frontiers in Neuroinformatics 10:50.
doi
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