Image segmentation is a part of medical image processing. Medical image segmentation means how the software takes a medical image and divides it into different meaningful parts. There is plenty of medical image segmentation software in the market. Some are free, some you have to buy in order to use. We will give you an idea about the top 5 free medical imaging segmentation software and how you can best access them.

SPM or Statistical Parametric Mapping

SPM was developed in the University College of London, the UK by its Welcome Department of Cognitive Neurology. This open-source software can be accessed by everyone. The primary purpose of this software is to analyze the brain imaging data sequences. This software supports different modalities of medical imaging e.g. MEG, EEG, PET, SPECT, fMRI, etc. This software uses unsupervised, statistical clustering for the purpose of image segmentation.


Oxford University’s Functional Magnetic Resonance Imaging of the Brain (FMRIB) developed FSL- the FMRIB Software Library. It runs on both Linux and Mac iOS and it’s free as long as it’s not being used for commercial purposes. This software library contains image analysis and statistical tools for MRI brain imaging data. This software uses an automated, brain extraction tool to do the segmentation of brain images.


Freesurfer is also an open-source software to analyze brain images. It was developed by CorTechs Lab and it uses both automatic and manual segmentation processes so that it can reconstruct the cerebral cortex from structural, MR images. It’s an important tool for functional brain mapping. Things that can be done using this software include fMRI Analysis, Tractography, Skullstripping, Subcortical Segmentation, etc. You can download it from GitHub.

ITK or Insight Segmentation and Registration Toolkit

ITK is an open-source, cross-platform application that was built for image analysis- mainly image segmentation and image registration. It’s written in C++, C, Fortran, and Python; it was developed by Insight Software Consortium and released initially in 2001. The segmentation includes different types of both low-level and high-level using watershed algorithms and deformable models.

3D Slicer

3D Slicer is another open-source application that runs on Windows, Mac, and Linux. It’s used for medical image analysis, medical image processing, and 3D visualization. 3D Slicer is one of the most popular free medical image analysis applications. It was built by MIT’s AI lab and it’s based on VTK and ITK. The image segmentation in 3D Slicer is done in both manual and semi-autonomous means. 3D Slicer is used in lots of different medical applications, e.g. Lung cancer, prostate cancer, COPD, neurosurgery, etc.


Since there are a lot of options to choose from, users sometimes get confused as to which software to use. We suggest you choose from one of these as they are the best but also look if it serves the purpose you are using it for.


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