there are two script files in /scripts called basicanalysis.m and setup.m to look at.

basicanalysis.m provides some code to perform model fitting, parameter estimation and decoding using the OP, LP and BD models.

setup.m lists all data setup and algorithm parameters. Things you might want to change are:
analysisIntervals - you need to specify one of these, specific to the data used. I've given the two necessary for LT1 and TM1. Comment out the one not used.
maxSpatialDimensionSize - changes the spatial discretisation.
maxNStates - maximum number of states possible, i.e. the prior over number of states is on the integers between 1 and this.
nParticles - number of SMC particles.
updateStepInterval - time step of HMM, in seconds.

The data to use are in the .mat files. For TM1 (T-maze), spike trains data are in spikepos.mat and position data in jasper_position.mat; for LT1 (linear track) spike trains data are in CA1.mat and CA3.mat (need both) and position in kenan_position.mat.