This is a collection of software designed to process high-resolution magnetic resonance images of the cerebral cortex.

If you use this work in an academic publication, please cite the relevant references (see doc/references.bib).

The source is organized in three components, from high-level to low-level:

• Scripts to do the high-level processing, under scripts/.
• A Python package, under python/highres_cortex/.
• A library and compiled executables, written in C++, under src/.

This package is compiled using the BrainVISA compilation system, which is an extension to CMake. Follow the instructions at http://brainvisa.info/repository.html#use_brainvisa_sources to clone the source tree. You need to include two lines in bv_maker.cfg in order to clone and compile highres-cortex. Here is a minimal bv_maker.cfg:

[ source $HOME/brainvisa/source/trunk ]
  + anatomist trunk
  git https://github.com/neurospin/highres-cortex.git master highres-cortex

[ build $HOME/brainvisa/build/trunk ]
  anatomist trunk $HOME/brainvisa/source/trunk
  + $HOME/brainvisa/source/trunk/highres-cortex

• AIMS version 4.5 or later (in development at the time of this writing, use the trunk version from SVN). This image processing library is distributed as part of BrainVISA.
• The VipHomotopic tool from the Morphologist image segmentation pipeline, distributed as part of BrainVISA.
• GSL (GNU Scientific Library).
• Boost version 1.49 or later.
• CMake version 2.6 or later, with its extension brainvisa-cmake (distributed with BrainVISA).
• Python version 2.6 or later.

The source code of this work is placed under the CeCILL licence (see LICENCE.CeCILL.txt). Compiled code that links to the GPL-licensed GSL forms a derivative work thereof, and thus must be redistributed under the GNU General Public Licence (see LICENCE.GPLv3.txt).