Software packages

This is a (non-exhaustive) list of software packages commonly used in (NHP) neuroimaging analysis. These were not submitted to PRIME-RE but are rather common in the field. Documentation will not be provided on this site, but can usually be found at the websites for the individual packages. For a similar (much better curated) list, see NITRC.

If you use any of these software packages for your published work, please make sure to credit the developers. In many cases this is even a prerequisite for using the software at all. Information on how to credit a resource will usually be available on the resource’s linked website. If this is not the case, and there is not an obvious methods paper you can cite, you should probably still mention the name (and url) of the tools you used when describing your methods. It increases reproducibility and recognizes the efforts of the developers that create these tools.

If you would like to have something added to this list, please let us know or fill out a new resource form.

Package               Usage                                                    
AFNI Universal (f)MRI
ANTs Registration
BrainVISA Anatomy
Brainvoyager Universal (f)MRI
CIVET Cortical surface analysis
Connectome Workbench Universal MRI
dcm2niix Convert dcm to nifti
DSI Studio Tractography
Freesurfer Universal MRI. Surface generation. Segmentation.
FSL Universal (f)MRI
Horos Dicom viewer. Open source OsiriX alternative
InVesalius 3D reconstruction
ITK-SNAP Segmentation and 3D
JIP Registration
Lead-DBS Connectome
MedInria Image processing and viewing
MIPAV Image processing and viewing
MRIcro(GL) Image viewing 3D
MRtrix3 Tractography
mrVista Universal (f)MRI
OsiriX DICOM viewer
Slicer 3D Versatile image processing 3D
SPM Universal fMRI
TrackVis Tractography

Python based solutions

Package               Usage                                                    
Pycortex Volumes and surfaces
NiPype Pipelines
NiPy A collection of more Python resources
Nilearn Statistical learning and plotting