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bet2

standalone Brain Extraction Tool (bet2) with python wrapper, released by http://fsl.fmrib.ox.ac.uk/

The following features are added:

  • The program is reconfigured using CMake
  • CMake configures MATLAB mex target as well.
  • Building static and dynamic library (dll or so) of BET
  • Support Windows and Linux

To build:

git clone https://github.com/aghaeifar/bet2.git
cd bet2
mkdir build
cd build
cmake ..
make -j4

To use MATLAB mex interface:

bet2_mex(input)

where input is a 3D single real array.

To use in Python:

import ctypes
handle = ctypes.CDLL(os.path.join(dir_path, "lib", "libbet2.so"))
handle.runBET.argtypes = [np.ctypeslib.ndpointer(np.float32, ndim=self.img_mag.ndim, flags='F'),
                np.ctypeslib.ndpointer(np.float32, ndim=len(mask_size), flags='F'),
                ctypes.c_int, ctypes.c_int, ctypes.c_int]
mask_size = mag.shape
mag = self.img_mag.copy(order='F')
mask = np.zeros(mask_size, dtype=mag.dtype, order='F')
handle.runBET(mag, mask, *mask_size)

where input is a 3D float32 real numpy array.

Precompiled mex files for Windows and Linux can be downloaded in the repository releases.