![]() | Spike Train Analysis Toolkit |
The Spike Train Analysis Toolkit requires:
The Toolkit has been tested on the following platforms (see the complete list of supported platforms):
neuroanalysis.org
.spike
will be created and all of files will reside there. For example, if you want your files to be located in /home/username/spike/
, move the archive to /home/username/
.Configure your MEX environment if you have never done so. This is done by starting Matlab and issuing the following command:
>> mex -setup
More detailed instructions are given at the MathWorks site. If you have not already done so, install the gsl
, signal
, and statistics
packages from Octave-Forge. This is done by downloading the named package archive, starting Octave, and issuing the following command:
octave:1> pkg install package-name
where package-name is replaced with the name of the downloaded package file. http://gnuwin32.sourceforge.net/downlinks/gsl.php
. This link will direct you to a local mirror. Note that Gsl for Windows is a pre-compiled 32-bit version of GSL version 1.8 (April 2006). If you're running a 64-bit Windows operating system, however, you will need to download and compile GSL yourself. To help with compilation using Microsoft Visual C++, you may like to use the project files provided by computer expert Brian Gladman, which builds GSL version 1.13 (September 2009). Then continue with step 3 of these instructions.C:\Program Files\GnuWin32
). For the remainder of the documentation, we will represent this folder as <gsl_folder>
.Start Menu > Control Panel > System
. Click on the Advanced
tab. Click the button Environment Variables
at the bottom of the tab. Add the following variables: Variable | Value |
INCLUDE | <gsl_folder>\include |
LIB | <gsl_folder>\lib |
user
or system
depending on the desired scope of the installation. mex -setup
command in Matlab will create a file called mexopts.bat
in the user account's Matlab folder (e.g., <user>\Application Data\Mathworks\MATLAB\R14\mexopts.bat
). set LINK_FILE
.libgsl.a libgslcblas.a
.mex -setup
after you modify this file, this change will be overwritten and must be repeated. ftp://ftp.gnu.org/gnu/gsl/
, or use your distribution's package management tools to install the GSL development package.libgsl.so
and libgslcblas.so
(e.g., /usr/local/lib/
) in LD_LIBRARY_PATH
.sudo ln -s /usr/lib/libstdc++.so.6.0.10 /usr/lib/libstdc++.so
), and link Matlab to this and the shared GCC libraries (e.g., /$MATLABPATH/sys/os/$ARCH/libstdc++.so.6
and /$MATLABPATH/sys/os/$ARCH/libgcc_s.so.1
should point to the libraries on your system with which the MEX files were compiled). >> cd /home/username/spike
help make
for additional options): >> make
demo/
directory, there is a script called staverify
that performs a set of calculations to verify that the installation was successful (you may also run make('check')
in Matlab or Octave). (Please note that if using Octave, the ctwmcmc_info
test will not check the confidence intervals. This is because of minor differences between the functions prctile
and random
, as implemented in Matlab versus Octave, which would otherwise cause the test to fail. While this does not constitute a critical failure, Octave's prctile
function, as implemented in the statistics package up to version 1.0.9, is known to have a bug.)staverify
, please take the time to add your system configuration to the list of our supported platforms.If you have difficulty with compilation of the toolkit, please first take a look at our troubleshooting guide. If you still need help, please contact us.