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.
|CIVET||Cortical surface analysis|
|Connectome Workbench||Universal MRI|
|dcm2niix||Convert dcm to nifti|
|Freesurfer||Universal MRI. Surface generation. Segmentation.|
|Horos||Dicom viewer. Open source OsiriX alternative|
|ITK-SNAP||Segmentation and 3D|
|MedInria||Image processing and viewing|
|MIPAV||Image processing and viewing|
|MRIcro(GL)||Image viewing 3D|
|Slicer 3D||Versatile image processing 3D|
Python based solutions
|Pycortex||Volumes and surfaces|
|NiPy||A collection of more Python resources|
|Nilearn||Statistical learning and plotting|