Blohm Lab Wiki

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
Open Broadcaster Software (free) for recording / editing / creating videos and live streaming
Pandoc (free) - the ultimate document converter (supporting all kinds of formats, including LaTeX, Markdown, DocX, etc)

Open Broadcaster Software (free) for recording / editing / creating videos and live streaming
Jitsi (free) secure fully featured video conferencing
Zoom video communications platform

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.

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