S1 kinematic encoding analysis

This repository contains analysis code relevant to the manuscript "Area 2 of primary somatosensory cortex encodes kinematics of the whole arm", which can be found here.

How to get the code

Using git

The best way to get the code is to clone this repository with git. When cloning the repository, make sure to use the -r flag to also clone the submodules in lib/.

git clone -r https://github.com/raeedcho/s1-kinematics.git

Downloading the release

You can also download the code from here.

Execution instructions

The main scripts used to generate the figures from the behavioral and neural data (found here) are plotRFMaps.m, twoworkspace_analysis.m, and actpas_analysis.m.

Before running the main analysis scripts, add lib/ and all its subdirectories to the MATLAB path. Download the data to disk and modify the dataroot at the top of the scripts to point to the unzipped data directory. Then simply run the scripts. Note that because these scripts use extensive cross-validation, the analysis will take a long time to run.

Environmental requirements

I've tested this code most recently on MATLAB 2019a with the following toolboxes installed (note that many of these toolboxes are not actually required for the code to run--this was just my most recent MATLAB environment):

• Simulink Version 9.3 (R2019a)
• Bioinformatics Toolbox Version 4.12 (R2019a)
• Communications Toolbox Version 7.1 (R2019a)
• Computer Vision Toolbox Version 9.0 (R2019a)
• Control System Toolbox Version 10.6 (R2019a)
• Curve Fitting Toolbox Version 3.5.9 (R2019a)
• DSP System Toolbox Version 9.8 (R2019a)
• Database Toolbox Version 9.1 (R2019a)
• Datafeed Toolbox Version 5.8.1 (R2019a)
• Deep Learning Toolbox Version 12.1 (R2019a)
• Embedded Coder Version 7.2 (R2019a)
• Filter Design HDL Coder Version 3.1.5 (R2019a)
• Fixed-Point Designer Version 6.3 (R2019a)
• Fuzzy Logic Toolbox Version 2.5 (R2019a)
• GPU Coder Version 1.3 (R2019a)
• Global Optimization Toolbox Version 4.1 (R2019a)
• HDL Coder Version 3.14 (R2019a)
• HDL Verifier Version 5.6 (R2019a)
• Image Acquisition Toolbox Version 6.0 (R2019a)
• Image Processing Toolbox Version 10.4 (R2019a)
• Instrument Control Toolbox Version 4.0 (R2019a)
• MATLAB Coder Version 4.2 (R2019a)
• MATLAB Compiler Version 7.0.1 (R2019a)
• MATLAB Compiler SDK Version 6.6.1 (R2019a)
• MATLAB Report Generator Version 5.6 (R2019a)
• Mapping Toolbox Version 4.8 (R2019a)
• Model Predictive Control Toolbox Version 6.3 (R2019a)
• Optimization Toolbox Version 8.3 (R2019a)
• Parallel Computing Toolbox Version 7.0 (R2019a)
• Partial Differential Equation Toolbox Version 3.2 (R2019a)
• Phased Array System Toolbox Version 4.1 (R2019a)
• Reinforcement Learning Toolbox Version 1.0 (R2019a)
• Robotics System Toolbox Version 2.2 (R2019a)
• Robust Control Toolbox Version 6.6 (R2019a)
• Sensor Fusion and Tracking Toolbox Version 1.1 (R2019a)
• Signal Processing Toolbox Version 8.2 (R2019a)
• SimBiology Version 5.8.2 (R2019a)
• Simulink 3D Animation Version 8.2 (R2019a)
• Simulink Check Version 4.3 (R2019a)
• Simulink Code Inspector Version 3.4 (R2019a)
• Simulink Coder Version 9.1 (R2019a)
• Simulink Control Design Version 5.3 (R2019a)
• Simulink Coverage Version 4.3 (R2019a)
• Simulink Design Optimization Version 3.6 (R2019a)
• Simulink Design Verifier Version 4.1 (R2019a)
• Simulink Report Generator Version 5.6 (R2019a)
• Simulink Requirements Version 1.3 (R2019a)
• Simulink Test Version 3.0 (R2019a)
• Stateflow Version 10.0 (R2019a)
• Statistics and Machine Learning Toolbox Version 11.5 (R2019a)
• Symbolic Math Toolbox Version 8.3 (R2019a)
• System Composer Version 1.0 (R2019a)
• System Identification Toolbox Version 9.10 (R2019a)
• Text Analytics Toolbox Version 1.3 (R2019a)
• Wavelet Toolbox Version 5.2 (R2019a)