Table of Contents

NeuroElf installation

Requirements

As said on the introduction page, NeuroElf requires one of the following environments:

Process

To install NeuroElf, please download the current version from the main page (either the installer or flat folder/snapshot).

For a video demonstration, please watch the video on the right side (go to the NeuroElf installation video page for a full-size view).

Using the installer

In case you downloaded the installer, unzip the archive to a temporary location, which contains three files:

The first .m file contains the code that unpacks the files from the .mat file within Matlab/Octave, runs some preliminary checks and, eventually, calls neuroelf_setup, which performs some of the setup tasks (e.g. compiling the MEX files if necessary and creating the file format cache). To install the toolbox, change the current directory in Matlab to the temporary folder where you unzipped the archive and then call the installing .m file with the -i input argument: 

% change into folder containing installer
cd ~/Desktop
 
% call installer (in this case for version v0.9c)
NeuroElf_v09c -i
 
% when using Octave, you must use
% NeuroElf_v09c -f
% to override the Matlab release check!

You will then be asked where to install the toolbox. Please make sure to choose a path/folder that is writable to the user(s) regularly using the toolbox!!

The folder into which the toolbox is installed will be added to Matlab/Octave path temporarily; in other words, if you wish to keep the toolbox on the path, please open the Path settings under File → Set Path… or, alternatively, issue the savepath command on the Matlab/Octave prompt.

In case the MEX files were not compiled on your platform and also not part of the installation package, please first read the page on MEX file compilation and, if that doesn't help, get in touch with me (see the error reporting page for instructions).

Using the flat folder/snapshot

In case you downloaded the flat folder or snapshot archive, simply unzip this archive to its final destination. The archive contains one folder which is named according to the version of the toolbox, e.g. NeuroElf_v09c.

To finalize the installation, change into the installation folder in Matlab and issue the neuroelf_setup function manually: 

% change into NeuroElf installation folder
cd /usr/local/matlab/toolbox/NeuroElf_v09b
 
% call NeuroElf's setup
neuroelf_setup

This time, you'll have to add the path manually and then save it, e.g. by issuing these commands:

neuroelf_addpath.m
% adding NeuroElf to the path and saving the altered path
addpath(neuroelf_path);
savepath;

Notes

Errors / warnings during installation

Given that the setup function (neuroelf_setup) will try to compile some C-based code into MEX files (see NeuroElf MEX files for infos), it is possible that you will see some warning or error messages in case your system doesn't have a functional compiler installed or setup in Matlab. These error messages should only occur the first time you set up a particular NeuroElf version!

In that case, the setup function will try to copy the MEX files that come with the package into the NeuroElf installation folder, after which all subsequent routines should work without further problems.

Note: On Windows machines that don't have a compiler installed, the mex function still asks to select a compiler and upon selecting “none” (0), the function exits without error. One user reported that it might be necessary to 1.) keep selecting 0 for each of the MEX files to be compiled, which is about 30 times, during the installation of NeuroElf (NeuroElf_v0XY -i internally runs neuroelf_setup) and then 2.) manually re-run the neuroelf_setup function again so that the MEX files are properly copied into the installation folder.

If you receive further warning/error messages about missing MEX files, the platform you're using is not supported (as of yet) by pre-built MEX files, and I would like to ask you to get in touch with me (at info _at_ neuroelf _dot_ net), so that I can add support for this platform by adding compiled files accordingly (for which I might require your assistance and some patience…).

Installation folder structure

Once the toolbox is installed and setup, the following folder structure should be present: