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.