Software Programming



  • 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