In this section we present a list of available software tools. If you have any question, please do not hesitate to contact us

Brain Skull Stripping Tool: stripTs

Description: This command line tool for Windows extracts the brain region from volumetric medical images of the head.
Skull stripping is performed by registration of an atlas and level-set-based refinement of the brain region. The tool works best if image and atlas are of the same modality, but different modalities are also possible.
For example you can use the Harvard SPL atlas with a customized brain mask. It is available at:


  1. volumetric image of the head region of which the brain area should be extracted (formats: .mha, .mhd)
  2. volumetric image of the atlas gray level image (formats: .mha, .mhd)
  3. volumetric label image of the brain region in the atlas (formats: .mha, .mhd)


  1. volumetric binary mask image of the brain region in the input image (format: .mha)
  2. volumetric stripped graylevel image of the brain region in the input image (format: .mha)

Architecture: Windows - Command line tool

Source code: The source code is available as a filter for the Insight Toolkit (ITK) from the Insight Journal at


A plug-in for Slicer is also available.

A more detailed description of the method can be found in the related publications at the SSBE meeting (arXiv:1204.0357) and in the Insight Journal.

BraTumIA is a software dedicated to multimodal image analysis of brain tumor studies. It performs volumetric segmentation of healthy and tumor tissues by employing multispectral MRI sequences (currently T1, T1-contrast, T2-contrast, and FLAIR). Segmented tissues include Gray Matter (GM), White Matter (WM), Cerebrospinal Fluid (CSF), necrotic core, edema, non-enhancing tumor and enhancing tumor. You can watch a video explaining the main features of BraTumIA here.

Note: The current version of BraTumIA is designed to work on pre-operative images.

Architecture: Windows - Graphical User Interface

Based on request BraTumIA is made available to researchers and clinicians, please register here:

Forum, RSS, news bulletin and others available at the BraTumIA's NITRC page:

BraTumIA software tool, Overlay of four MRI modalities used to jointly segment healthy and four-layer tumor tissues.

iSix is a plugin for the popular MacOs software Osirix. It allows the user to perform manual and semi-automatic segmentation using: different size brushes, region growing, and livewire segmentation. 

For MRI studies using Dixon sequences, it incorporates a dedicated module to quantify amount of fat and muscle in the tissues.

Segmentations can be saved in .STL and MetaImage formats (.mha/.mhd).

iSix is available for free for research purposes:

Description: FISICO is a software tool to perform fast segmentation corrections of medical images. The tool allows the user to load existing segmentations and corresponding images, and perform in-plane contour corrections that are transformed into 3D shape updates through a fast free-form deformation model, enabling with this a considerable improvement in the time necessary to correct segmented images. 

The corrected output can be saved in any ITK-compatible format  (e.g. .nii, .mha, .hdr, etc.) as well as Dicom.

Architecture: Windows 7/8 and MacOS 10.10 or superior.

YouTube video:

Main interface of FISICO. Typical three-panel views and 3D visualization. The user loads a segmentation to be corrected and the original image. Using simple contour corrections, 3D shape corrections are generated and presented to the user on the 3D view. Optionally, if a ground-truth is available the dice coefficient can be calculated (excellent for training of radiologists, or analysis of existing automatic segmentation tools). 

Description: This is an extension of the diffeomorphic demons algorithm for multimodal image registration. The options of the command-line tool is same as the one for monomodal registration, except that the histogram matching option has been removed and several default parameters have been changed.

Architecture:Windows XP - Command line tool

Description: Di2Mesh is a GUI-based application allowing the user to compute surface-to-surface distances and visualize them using a colormap. Different distance metric schemes are available, such as closest point to mesh, iterative closest point, and thin plate spline deformation and CPS transformations based on user-provided landmarks. In this case, the software allows the user to interactively select anatomically corresponding landmarks, which are used to perform an elastic transformation. A closest-point computation is then performed to establish corresponding points. Original positions are then connected to these corresponding points and used to measure Euclidean distances.

Feel free to download the quick user guide below to see example of features in the software!

Description: This Windows command line tool performs fully automatic segmentation of tissues (cerebrospinal fluid, gray matter, white matter) in MR images of healthy subjects. It requires a skull-stripped volumetric T1-weighted image. We recommend to use the stripTs tool from this website for skull-stripping.

The usage is described in the readme file, which is located in the zip folder for download.

Architecture: Windows 64 bit - Command line tool (min 16GB RAM)

Related publication