Skip to main content

MRI visualization software


The following software are free to download and use.


3D Slicer

Software can import and export DIOM images along with NIFTI images. There are hundreds of extensions available to install. It also allows Python scripting with live introspection and interface scripting. However, even the basic package has great functionality built into it and enables 3D visualization with a default three orthogonal pane view. 

3D Slicer

Available for Windows, MacOS and Linux



MIPAV is a great tool for basic visualization and image processing. It is also highly extensible, as one can write Java modules to incorporate into MIPAV. Another excellent feature of this tool is how simple it is to overlay one image ("image B") onto another image ("image A") and then change the transparency between the two. The interface is relatively clean and unobtrusive. 




ImageJ can be used for a variety of image processing tasks, including image segmentation, image registration and image analysis. It also has a large library of plugins that can be used to extend its functionality. FIJI is a "batteries included" distribution of ImageJ that bundles a large number of plugins.



ImageJ will run on any machine that has a Java Runtime Environment (Linux, MacOS and Windows)


MITK workbench

MITK (Medical Imaging Interaction Toolkit) is a free, open-source software for the development of interactive medical image processing software. It provides a wide range of functionality for image processing, visualization and analysis, including: filters, registration, segmentation and visualization.

MITK Workbench

MITK will run on Windows, Linux and MacOS



FSLEyes is part of the FSL package. To use FSLEyes, the FSL package would typically have to be installed. FSLEyes is a 3D and 4D image viewer for neuroimaging data. It can load NIFTI, MGH, GIFTI, Freesurfer and VTK files. FSLeyes can be used to view functional MRI (fMRI) data, structural MRI data, and diffusion tensor imaging (DTI) data. It also has the ability to view FEAT analyses.


FSLEyes will run on MacOS and Linux. There is more work required to get it to run on Windows (WSL)



ITK-SNAP is a free and open-source software for medical image segmentation. It provides a set of tools to make segmentation of volumetric data easier and faster. SNAP is very good for image segmentation and provides tools for hand contouring and for cleaning up the results of automatic segmentation. It also has a powerful level set segmentation algorithm to segment anatomical structures in three dimensions. In addition to segmentation, ITK-SNAP also provides tools for image navigation, registration and post-processing. It supports a wide range of image formats, including NIfTI and DICOM.


ITK-SNAP will run on Windows, MacOS and Linux