MR Image Processing

FSL (FMRIB Software Library)

A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. It runs on Apple and PCs (both Linux, and Windows via a Virtual Machine)


A software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.  It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging.

FreeSurfer provides a full processing stream for structural MRI data, including:

  • Skull stripping, B1 bias field correction, and gray-white matter segmentation
  • Reconstruction of cortical surface models (gray-white boundary surface and pial surface)
  • Labeling of regions on the cortical surface, as well as subcortical brain structures
  • Nonlinear registration of the cortical surface of an individual with a stereotaxic atlas
  • Statistical analysis of group morphometry differences

AFNI (Analysis of Functional NeuroImages)

A set of C programs for processing, analyzing and displaying functional MRI (fMRI) data. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, Mac OS X. It is available free (in C source code format, and some precompiled binaries, also Matlab m files) for research purposes.

Link here for installation files: (page may be slow to load)

For easy install of precompiled version go to:

This software performs very well on Windows 10 command line without need for virtual machine or dual boot install. Activate developer tools for Ubuntu linux on Windows here:h ttps://


Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM.  The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI ,PET, SPECT, EEG and MEG.

NMR Spectrum Processing

A data processing version of the NMR software used on all Bruker instruments is available to academic and government institutions for download. It has TopSpin functionality, but does not support direct processing of data acquired through ParaVision. MRS data acquired using ParaVison can be exported to TopSpin during instrument runs for processing offline using this software.