gift-surg / MRImultiAtlasForNeonatalRabbitBrain

Code for the benchmarking and validation of the Neonatal Rabbit brain Multi-Atlas

MRI Multi-Atlas For the Neonatal Rabbit Brain

Repository with the Python code for the benchmarking and validation of the Neonatal Rabbit brain Multi-Atlas proposed in the Neuroimage paper. Dataset can be found here. To use the multi-atlas for the automatic segmentation of a new dataset please consider the repository SPOT-A-NeonatalRabbit.

How to use

• Requirements

  • Python 2 (Python 2 only for the current release)
  • Install SPOT-A-NeonatalRabbit and related dependencies
  • Download the data from the zenodo repository

• Setup

  • After downloading the dataset, set the path in the python module ./path manager.py as indicated in the comments. In this module you will find the only paths that you will need to change.
  • As a research software, sometimes important indications are annotated into comments inside the code.

• Usage

  • We suggest to install the required libraries in a virtual-environment.
  • Each module in the project structure can be run independently from command line.

Code testing

The core methods are in the external libraries. Run the tests of LABelsToolkit and SPOT-A-NeonatalRabbit before starting.

Support and contribution

Please see the contribution guideline for bugs report, feature requests, code re-factoring and re-styling.

Authors and Acknowledgments

• The MRI Neonatal Rabbit Multi-Atlas and related code is developed within the GIFT-surg research project, a collaborative project between the University College London (UK) and Katholieke Universiteit Leuven Leuven (Belgium).
• This work was supported by Wellcome / Engineering and Physical Sciences Research Council (EPSRC) [WT101957; NS/A000027/1; 203145Z/16/Z].
• The full list of authors and acknowledgments can be found in the Neuroimage paper, please use the same reference to cite the dataset and the code if you find it useful for your research.