QMRTools
QMRTools: a Mathematica toolbox for quantitative MRI analysis. - Published in JOSS (2019)
fsbrain
R library for structural neuroimaging. Provides high-level functions to access (read and write) and visualize surface-based brain morphometry data for individuals and groups.
https://github.com/bluebrain/bioexplorer
The Blue Brain BioExplorer (BBBE) is a tool for data visualization experts and scientists to extract and analyze scientific data from visualization and interactive exploration
freesurferformats
GNU R package for reading and writing neuroimaging file formats. Not limited to FreeSurfer anymore, despite its name.
https://github.com/dipy/dipy
DIPY is the paragon 3D/4D+ medical imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.
csg_mri_pipelines
MRI preprocessing and analysis pipelines and tools for the study of disorders of consciousness