This folder contains the source code for image processing steps described in the paper:

@inproceedings{crimi2013semi, title={Semi-automatic classification of lesion patterns in patients with clinically isolated syndrome}, author={Crimi, Alessandro and Commowick, Olivier and Ferr{'e}, Jean-Christophe and Maarouf, Adil and Edan, Gilles and Barillot, Christian}, booktitle={2013 IEEE 10th International Symposium on Biomedical Imaging}, pages={1102--1105}, year={2013}, organization={IEEE} }

This script assumes that the skull has already been stripped (e.g. with the bet script of FSL). The given files are:

• nyul_standardization.cpp and nyul_standardization.h The core algorithm is given by these files.

• test_nyul.cpp An example program which expects as inputs two 3D volumes given as NIFTI or Analyze files.

• Make and CMake files (CMakeLists.txt) use "ccmake" . and then "make"

Requirements: ITK library 3.x version, future versions might have compability issues.

How to run it: nyul_standardization reference.nifti input.nifti The test data are taken from the free ICBM dataset

All code is given freely as GNU/General Public License v. 3.0 https://www.gnu.org/licenses/gpl-3.0.html