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+# Striatum Model from Humphries, Wood and Gurney (2010) PLoS Comp Biol
+
+This is a complete set of code required to run and analyse the striatum model from Humphries, Wood and Gurney (2010) *PLoS Computational Biology*. The code is freely available for study and modification. Please cite the original sources. For questions and assistance contact:  
+m.d.humphries@shef.ac.uk or drmdhumphries@gmail.com
+
+---
+
+## Top-level Files
+
+- **Experiment_RandomInput.m:**  
+  The top-level function that runs the model for the results in Fig 9 of the paper; this contains a selection of frequently changed parameters. Extensions to the model should be based on this file.
+
+- **Experiment_ImpactOnCentreMSN.m:**  
+  The top-level function that runs the model for the results in Fig 10 of the paper; extended to include stimulation of a sub-set of MSNs and FSIs residing a specified spherical shell a set distance from the selected target MSN. This needs to load a 1mm³ network, with 1% FSIs, to run the experiments. This 129MB file `.mat` is available from:  
+  [http://www.abrg.group.shef.ac.uk/code/Striatum/Striatum_network_1000-1000-1000_num_1_at_734299.3923.mat](http://www.abrg.group.shef.ac.uk/code/Striatum/Striatum_network_1000-1000-1000_num_1_at_734299.3923.mat)
+
+- **StriatumNetworkParameters.m:**  
+  The complete specification of the model; a few of the parameters set here are overwritten in `Experiment_RandomInput.m` or `Experiment_ImpactOnCentreMSN.m`.
+
+- **RunSimulation.m:**  
+  Function called by `Experiment_RandomInput.m` (or `Experiment_ImpactOnCentreMSN.m`) to handle passing the parameters to the MEX file that runs model simulation.
+
+- **checkStriatumInputs.m:**  
+  Ensures that all parameters are of the right class and type for handing to the MEX function (called by `RunSimulation.m`).
+
+---
+
+## ./CreateNetwork (folder)
+
+- **BuildStriatumNetwork.m:**  
+  Builds the network model according to the specified parameters (called by `StriatumNetworkParameters.m`); uses the probability of intersection functions supplied by the 4 `.mat` files in this folder.
+
+- **GetNeuronPositions.m:**  
+  Puts all neurons in their 3D positions, ensuring that none are closer than the minimum set distance (called by `BuildStriatumNetwork.m`).
+
+---
+
+## ./Simulation (folder)
+
+This contains the MEX files and source C code for the simulation engines that run the model. The simulation uses the `striatum_RK2` MEX file, solving the ODEs using the midpoint method (aka 2nd order Runge-Kutta).
+
+The RK2 method MEX files are provided compiled for 32-bit (`.mexw32`) and 64-bit (`.mexw64`) Windows, and for 64-bit (`.mexa64`) Linux systems. We strongly recommend that you recompile the MEX code from the source C++ for your platform.
+
+---
+
+## ./Analyses (folder)
+
+- **firing_stats_solo.m:**  
+  Analyses of the firing properties of a simulation, including firing rate distributions.
+
+- **analyse_centre_MSN.m:**  
+  Impact of inputs on centre MSN.
+
+- **raster_plot.m:**  
+  Helper function for the analyses. Plots rasters of spike-train data.
+
+---
+
+## Notes
+
+1. This code represents version 1.5 of our striatal model: it combines the new 3D connectivity model with the neuron and gap junction models from version 1 (published in Humphries et al, 2009; ModelDB ID:128874).
+
+2. This code does not include our updated model of dopamine's effects on the MSN (Humphries, Lepora, Wood & Gurney, 2009b).
+
+---
+
+## References
+
+Humphries, M. D., Wood, R. & Gurney, K. (2009) Dopamine-modulated dynamic cell assemblies generated by the GABAergic striatal microcircuit. *Neural Networks*, 22, 1174-1188. Download at:  
+[http://dx.doi.org/10.1016/j.neunet.2009.07.018](http://dx.doi.org/10.1016/j.neunet.2009.07.018)
+
+Humphries, M. D.; Lepora, N.; Wood, R. & Gurney, K. (2009b) Capturing dopaminergic modulation and bimodal membrane behaviour of striatal medium spiny neurons in accurate, reduced models. *Frontiers in Computational Neuroscience*, 3, 26. Download at:  
+[http://dx.doi.org/10.3389/neuro.10.026.2009](http://dx.doi.org/10.3389/neuro.10.026.2009)
+
+Humphries, M. D., Wood, R. & Gurney, K. (2010) Reconstructing the three-dimensional GABAergic microcircuit of the striatum. *PLoS Computational Biology*, 6, e100101. [PDF copy included]
+
+---
+
+2025-06-20: Converted README to Markdown.