software_packages.md

<style> .dropbtn {background-color: #1e6bb8; color: white; padding: 16px; font-size: 1rem; border: none; cursor: pointer; width: 30rem} .dropbtn:hover, .dropbtn:focus {background-color: #2980B9;} .dropdown {position: relative; display: inline-block;} .dropdown-content {display: none; position: absolute; background-color: #f1f1f1; min-width: 100%; overflow: auto; box-shadow: 0px 8px 16px 0px rgba(0,0,0,0.2); z-index: 1; text-align: center; font-size: 1rem;} .dropdown-content a { color: black; padding: 12px 16px; text-decoration: none; display: block;} .dropdown a:hover {background-color: #ddd;} .show {display: block;} .dropbtn + .dropbtn { margin-left: auto; } @media screen and (min-width: 64em) { .dropbtn { max-width: 64rem; width: 40rem; padding: 0.75rem 1rem; } } @media screen and (min-width: 42em) and (max-width: 64em) { .dropbtn { width: 30rem; padding: 0.6rem 0.9rem; font-size: 0.9rem; } } @media screen and (max-width: 42em) { .dropbtn { display: block; width: 20rem; padding: 0.75rem; font-size: 0.9rem; } .dropbtn + .dropbtn { margin-top: 1rem; margin-left: 0; } } </style>

Select Resource Category

Templates & atlases General analysis Structural analysis Functional analysis Diffusion analysis Cross-species analysis Data sharing Software packages Hardware & protocols

<script> function myFunction() {document.getElementById("myDropdown").classList.toggle("show");} window.onclick = function(event) { if (!event.target.matches('.dropbtn')) { var dropdowns = document.getElementsByClassName("dropdown-content"); var i; for (i = 0; i < dropdowns.length; i++) {var openDropdown = dropdowns[i]; if (openDropdown.classList.contains('show')) {openDropdown.classList.remove('show'); } } } } </script>

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