MATLAB code for studying neural recording data from monkey as performs manual and brain control target pursuit tasks. Data from Moritz lab. Orignally studied by Charlie Matlack (cmatlack@uw.edu).
Dependencies: makes use of functions in the stats toolbox.
In preprocess:
- Functions for importing data from .nev and .nsx files.
- Functions for importing trial data from Labview (.mat) files.
- Functions for smoothing torque data, and converting spike times to binned spikes
- generate_glm_data.m for simulating a GLM given input data and filters
In models:
- If the GLM has the form: E(y) = g(X\beta) where X is a data matrix and \beta is a vector of filter coefficients, this directory contains functions for taking raw data and preparing data matrix to be input into a GLM, along with output vector y.
In eval:
- Functions to fit the filter coefficients beta
- Functions to predict spike trains given stimulus and a fit GLM
- Functions to plot filters of GLM
- Other plotting functions
In functions:
- Functions to import blackrock files
- Functions by Charlie to compute correlations, etc
- Functions to save plots as .eps
- Some other things
In other:
- Other people's GLM code
In old:
- Old code
In worksheets:
- Some scripts that make use of all this code
If MATLAB is started in the ./matlab directory then startup.m will automatically add the above directories to the path. It will try to add the Chronux functions by adding ~/matlab/chronux to the path, and will try to add the .nev and .ns3 files to the path by looking in ./matlab/blackrock, but these are not necessary.
See ./matlab/accessing_data.txt for information on the format of matlab, labview and BlackRock files
0.3 -- Can now:
-Compute Granger causality for a recording -Estimate a range of intentional and non-intentional GLMs -Use raised cosine basis vectors for spike history filters -Added concept of experiment stuctures, allowing the study of entire year's worth of recordings with createExperiment, setupExperiment and runExperiment functions
0.2 -- Updated to include code to run LN model, and a basic version of a GLM model
0.1 -- contains a whole bunch of functions to compute correlation (corr_*.m) bw firing rate and torque (cursor) position/vel/accel. Not needed, as superseded by correlation_nev.m. Will be dropped from future versions.