This is a list of commonly used software packages for analysis of neuroimaging data. Please feel free to expand.

FSL: Software for analysis of neuroimaging data for Linux and Mac (can be run on Windows on a virtual machine)

SPM: Matlab-based software for analysis of neuroimaging data. Runs on Linux, Windows, MacOS

mrTools: Matlab-based software for analysis of neuroimaging data. Runs on Linux, Windows, MacOS

AFNI: Software suite for analysis of neuroimaging data for Linux and Mac (can be run on Windows on a virtual machine)

FreeSurfer: Software for cortical surface extraction and analysis

BrainVoyager: Commercial software for analysis of neuroimaging data and cortical surface extraction and analysis. Cross-platform

Containerised Environments: A brief guide on how to create containerised environments to run any analysis pipeline on a high-performance computing cluster.