NeuroNerds

Useful links for NeuroNerds looking to learn coding.

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General Links

• Brainhack101 Slides
• NeuroLinks Portal for Resources
• Online Brain Intensive Video Lectures
• Greg's info (to ask questions)

Challenges and Tools

Code Versioning and Sharing

• GitHub
• GitHub Guides

Code Execution and Portability

• Docker
• Docker Getting Started
• Singularity

Reproducible Execution

• Jupyter Notebook
• Binder

Choosing your Language

Desiderata	Matlab	Python
Numerical Processing	✔️	✔️
Complete Programming Language	✖️	✔️
Large User Community	✔️	✔️
Lots of Available Libraries	✔️	✔️ ✔️
Open Source	✖️	✔️
Works out-of-the-box	✔️ ✔️	✖️

MATLAB

Software:

• MATLAB
• GNU Octave (free altnernative to MATLAB)

Tools/Resources:

• Learn to code with MATLAB
• Statistical Parametric Mapping Toolbox (SPM12)
• NeuroImaging Analysis Kit (NIAK)
• Pipeline System for Octave and MATLAB (PSOM)

Demo:

• Fun MRI Reconstruction

Python

Software:

• Python

Tools/Resources:

• Learn Python
• NeuroImaging for Python (Nipy)
• Configurable Pipeline for Analysis of Connectomes (CPAC)
• Diffusion in Python (Dipy)
• NeuroData MRI to Graphs Pipeline (ndmg)
• Nilearn
• Plotly, Plotly Offline (free)
• Scipy, Numpy, Scikit-learn, Scikit-image

Demo:

• Science In The Cloud
• Scipy Lectures

Misc Other

• HomeBrew (Installs a bunch of cool packages for Mac)