MIALSRTK: Super-resolution reconstruction of fetal MRI
Copyright © 2016-2017 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland
This software is distributed under the open-source BSD 3-Clause License. See LICENSE file for details.
The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ image processing tools necessary to perform motion-robust super-resolution fetal MRI reconstruction. This toolkit, supported by the Swiss National Science Foundation (grant SNSF-141283), includes all algorithms and methods for brain extraction , intensity standardization [1,2], motion estimation and super-resolution  developed during my PhD. It uses the CMake build system and depends on the open-source image processing Insight ToolKit (ITK) library, the command line parser TCLAP library and OpenMP for multi-threading. The USAGE message of each tool can be obained using either the -h or --help flag.
A Docker image is provided to facilitate the deployment and freely available @ Docker store.
The MIALSRTK can be downloaded here.
Please acknowledge this software in any work reporting results using MIALSRTK by citing the following articles:
 S. Tourbier, C. Velasco-Annis, V. Taimouri, P. Hagmann, R. Meuli, S. K. Warfield, M. Bach Cuadra, A. Gholipour, "Automated template-based brain localization and extraction for fetal brain MRI reconstruction", Neuroimage (2017) In Press. DOI
 S. Tourbier, X. Bresson, P. Hagmann, R. Meuli, M. Bach Cuadra, "An efficient total variation algorithm for super-resolution in fetal brain MRI with adaptive regularization", Neuroimage 118 (2015) 584-597. DOI