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MICCAI Best Paper Prizes for CMIC - Athens 2016

Congratulations to Luis Garcia-Peraza Herrera and Ester Bonmati who won respectively first and second prizes for best paper (the Kuka Best Paper Prize) at the MICCAI CARE (*) workshop! Well done!

Published: Oct 19, 2016 12:42:31 PM

TIG raising funds for Bliss

Luis Garcia-Peraza Herrera, Michael Ebner and Stefano Moriconiare (GIFT-surg project) are supporting Bliss for babies born premature or sick. Following on their Pub quiz  night at Mully's Basement Bar on the 15th September 2016 - they are running the Royal Parks Half Marathon (9th October 2016, London).


Published: Oct 6, 2016 4:22:54 PM

CMIC will be at MICCAI 2016 in Athens

Many papers and posters accepted accross CMIC at MICCAI main programme and satellites workshops. Check them out in Athens (17-21st October 2016)

Published: Oct 6, 2016 4:07:08 PM


CMIC Software and Open Source Database

CMIC is developing several software tools that will be of interest to the wider medical imaging community. Here we give a brief overview of our well established software packages such as TOAST and Camino and our rapidly advancing translational imaging platform NifTK.

In addition to software, we also provide access to the MIRIAD database. More information can be found here.

NifTK - A translational imaging platform

NifTK is the name of our platform, combining NiftyReg, NiftySim, NiftyRec and NiftySeg via the viewer NiftyView.  The aim is to take the tools that CMIC develops, and apply them in a clinical context. If you have any questions about the NifTK platform, please contact our CMIC Software Manager Matt Clarkson. The following sections provide more detail:



NiftyReg contains programs to perform rigid, affine and non-linear registration of medical images. Two versions of the algorithms are included, a CPU- and a GPU-based implementation. Further information about the method can be found here. Contributors include Marc Modat, Pankaj Daga and Sebastien Ourselin.

Download here



NiftySim is a solver for non-linear elastic or visco-elastic deformation. Two versions of the algorithms are included, a CPU- and a GPU-based implementation. Contributors include Zeike Taylor, Marc Modat, Lianghao Han, Stian Johnsen and Sebastien Ourselin

Download here



NiftyRec is a software package for fully 3D Stochastic Emission Tomographic Reconstruction. The package includes a Matlab Toolbox with inline documentation and a library for for C/C++ development. Computationally intensive tasks have a GPU implementation based on CUDA. Currently MLEM, OSEM, and OSL-MAPEM reconstruction algorithms are supported. Contributors include Stefano Pedamonte,  and Sebastien Ourselin.

Download here



NiftySeg is an open-source software package for image segmentation, bias field correction and cortical thickness estimation. Image segmentation is based on an Expectation-Maximisation algorithm with a Markov random field for local consistency and an improved sulci delineation enhancement. Cortical thickness is measured using a Laplacian based metric within a Lagrangian-Eulerian framework. Contributors include Jorge Cardoso, Marc Modat, Matt Clarkson and Sebastien Ourselin.

Download here


NiftyView is a cross platform graphical user interface, providing an entry point to the above packages, and in addition, many of the usual features you would find in any medical image viewer. NiftyView provides a working environment for our clinical collaborators, and research scientists. Contributors include Matt Clarkson, Gergely Zombori, Miklos Espak, John Hipwell, Steve Thompson and Sebastien Ourselin.

Independent Software Packages

In addition to the above platform, CMIC has developed:



TOAST is a software suite for image reconstruction in optical diffusion tomography (ODT). The toolbox consists of a set of MATLAB functions, both in the form of compiled mex files that link directly into the TOAST libraries, and Matlab scripts that perform high-level tasks in modelling, reconstruction and vis-ualisation. Contributors include Martin Schweiger and Simon Arridge.

Download here.



Camino is a free, open-source, object-oriented software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping. Contributors include most of Danny Alexander's group. 

Download here


FEB3 FEB3 (pronounced Phoebe) is a scalable, open-source, numerical analysis software founded on the Finite Element and the Isogeometric Analysis methods. It provides a framework of numerical solvers capable of simulating three-dimensional nonlinear physics, spanning from static and dynamic solid mechanics to parabolic and multiscale problems. FEB3 also features complete analyses for popular biomedical applications, such as angiogenesis, cancer development and wound healing. In addition, FEB3 facilitates inverse finite-deformation analysis modelling. The primary developers are Vasileios Vavourakis and Peter Wijeratne.

Download here.

Page last modified on 09 feb 16 15:51