definitions.py

import os

# PATHS
ROOT_DIR = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))

# LINEAR REGISTRATION HYPER-PARAMETERS
reg_aladin_LP = 2  # Number of levels to use to run the registration once the pyramids have been created.

# NONLINEAR REGISTRATION HYPER-PARAMETERS
reg_f3d_JL = 0.0001  # Weight of log of the Jacobian determinant penalty term
reg_f3d_BE = 0.005  # Weight of the bending energy (second derivative of the transformation) penalty term
reg_f3d_MAXIT = 250  # Maximal number of iteration at the final level
reg_f3d_LN = 4  # Number of level to perform
reg_f3d_LP = 3  # default 3; we do only the lp first level of the pyramid
reg_f3d_GRID_SPACING = -5.0  # Final grid spacing along the x, y, z axes in mm (in voxel if negative value), corresponds to -sx option in reg_f3d
reg_f3d_LNCC = 5.0  # Standard deviation of the Gaussian kernel.
reg_f3d_INTERP = 1  # Interpolation order (0=NN, 1=linear, 3=cubic)

# RESAMPLING
RESAMPLE_METHOD = 0  # 0: nearest neighbor interpolation on label map, 1: (smoothing and) linear interpolation on one-hot encoded labels

# RESAMPLING HYPER-PARAMETERS
SIGMA = 0  # Standard deviation of the Gaussian kernel used to smooth the label maps before resampling, only applies to RESAMPLE_METHOD = 1

# Local Normalized Cross-Correlation (LNCC) DISTANCE
LNCC_SIGMA = [-2.5, -2.5, -2.5]  # Standard deviation of the Gaussian kernel used to smooth the images in mm (if > 0) or in voxels (if < 0)

# WEIGHTS CALCULATION
WEIGHTS_TEMPERATURE = 0.15  # Temperature parameter for the conversion from LNCC distance to weights

# seg_EM (Expectation-Maximization to update the tissue prior)
seg_EM_MAXIT = 30  # Maximal number of iterations
seg_EM_MINIT = 3  # Minimal number of iterations
seg_EM_BIAS_ORDER = 4  # Order of the bias field
seg_EM_BIAS_THRESH = 0.05  # Threshold to stop the bias field estimation
seg_EM_MRF_BETA = 0.1  # Weight of the MRF prior

# WHETHER To USE PREVIOUS RESULTS OF REGISTRATION, RESAMPLING, AND WEIGHTS CALCULATION
USE_OLD_RESULTS = True

# MULTIPROCESSING FOR LOOP OVER ATLASES
MULTIPROCESSING = True
NUM_POOLS = 2  # More pools will require more RAM, be careful not to exceed the available RAM

# IN EACH OF THE ABOVE PROCESSES, HOW MANY SUBPROCESSES should reg_aladin and reg_f3d run in parallel?
OMP = 8  # OMP*NUM_POOLS should not exceed the number of cores available

# NIFTYREG AND NIFTYSEG PATHS
NIFTYREG_PATH = "/usr/local/bin"  # should contain reg_aladin, reg_f3d, reg_resample binaries
NIFTYSEG_PATH = "/usr/local/bin"  # should contain seg_EM binary