- FreeSurfer: an open source software suite for processing and analyzing (human) brain MRI images.
- FMRIB Software Library (FSL): a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data
- Diffusion Toolkit: a set of command-line tools with a GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images and does the preparation work for TrackVis.
- TrackVis: a software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography.
- AFNI - useful for some quick seed-based resting-state FMRI analysis.
- Neuroimaging in Python (NiPy): software projects in Python including:
- nipy: a python project for analysis of structural and functional neuroimaging data.
- dipy: a free and open source software project for diffusion MRI analysis.
- nitime: a library for time-series analysis of data from neuroscience experiments.
- pbrain: a collection of applications for the analysis of EEG and medical image data.
- nibabel: I/O files that provide read and write access to some common medical and neuroimaging file formats
- nipype: an open-source project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow.
- DSI Studio: a software that performs q-space diffusion MRI reconstruction, tractography and visualization.
- Osirix: DICOM images viewer.
- Medical Image Processing, Analysis, and Visualization (MIPAV): an application enables quantitative analysis and visualization of medical images of numerous modalities.
- ImageJ: a public domain Java image processing program.
- Git: a free and open source distributed version control system
- Emacs: an extensible, customizable text editor.
- vi: screen-oriented text editor originally created for the Unix operating system.
- Ipython Notebook: a web-based interactive computational environment that combines code execution, text, mathematics, plots and rich media into a single document.
Additional Useful Codes from Other Research Groups