Software
Contents
General
- Git (free) - version control software and Dmytro's tutorial
- Total Commander (free) - file manager
- WinSCP (free) - file transfer tool
- Mendeley reference manager (AVOID! Use Zotero instead!!!) - manage references & automatic bibliography generator for MSWord, LibreOffice and BibTeX
- Zotero (free) article and biography manager for Word, LibreOffice, and Google Docs
- SeaMonkey (free) - internet application suite including web editor
Text Editors
- TeXnicCenter (free) - LateX editor
- LyX (free) - graphical document processing interface using LaTeX
- Atom - Customizable text editor by GitHub. Allows for real-time collaboration (!) and has not-too-clumsy Git integration.
- Spacemacs - A distribution of Emacs, at the deep end of customizable text editors. Emacs has many "modes"; the most useful is probably Org mode, which is a kind of outliner+agenda that can be used to rapidly create LaTeX/Beamer files, and for literate programming (think Jupyter), among other uses. Compared to plain Emacs, Spacemacs starts with a better configuration that is more modular and easier to customize, and allows for the (optional) use of Vim keybindings.
Imaging Analysis
- SPM (free) - general purpose (fMRI oriented)
- PDC (free) - partially directed coherence analysis
- FieldTrip (free) - general purpose (EEG/MEG oriented)
- Brainwave (free) and documentation - MEG analysis toolbox
- CARET (free) - anatomical reconstruction toolkit for structural and anatomical data (simple tutorial)
- Atlas for identifying brain regions / function based on fMRI meta-analyses
Machine Learning
- Kevin Murphy's Kalman filter toolbox (free)
- libSVM - Support Vector Machine Library
- Andrew Ng's ML Programming Exercises
Vector Graphics
Statistics
- statcheck - Use this to check papers for errors in statistical reporting!
- SPSS - general purpose
- R (free) - general purpose with great online book!
- psignifit (free) - psychometric function fitting
- JASP (free) is especially useful for Bayesian stats!
