Create 3DParams.yaml

3DParams.yaml

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+imageType:
+  Original: {}
+  # Wavelet: {}
+  # LoG: {}
+  # Square: {}
+  # SquareRoot: {}
+  # Logarithm: {}
+  # Exponential: {}
+  # Gradient: {}
+  # LBP2D: {}
+  # LBP3D: {}
+
+featureClass:
+  firstorder:
+    - 'Energy'
+    - 'TotalEnergy'
+    - 'Entropy'
+    - 'Minimum'
+    - '10Percentile'
+    - '90Percentile'
+    - 'Maximum'
+    - 'Mean'
+    - 'Median'
+    - 'InterquartileRange'
+    - 'Range'
+    - 'MeanAbsoluteDeviation'
+    - 'RobustMeanAbsoluteDeviation'
+    - 'RootMeanSquared'
+    # - 'StandardDeviation'
+    - 'Skewness'
+    - 'Kurtosis'
+    - 'Variance'
+    - 'Uniformity'
+  shape:
+    - 'MeshVolume'
+    - 'VoxelVolume'
+    - 'SurfaceArea'
+    - 'SurfaceVolumeRatio'
+    - 'Sphericity'
+    # - 'Compactness1'
+    # - 'Compactness2'
+    # - 'SphericalDisproportion'
+    - 'Maximum3DDiameter'
+    - 'Maximum2DDiameterSlice'
+    - 'Maximum2DDiameterColumn'
+    - 'Maximum2DDiameterRow'
+    - 'MajorAxisLength'
+    - 'MinorAxisLength'
+    - 'LeastAxisLength'
+    - 'Elongation'
+    - 'Flatness'
+  glcm: # all features
+  glrlm: # all features
+  glszm:
+  gldm: # all features
+  ngtdm:
+
+setting:
+  # Feature Extractor Level
+  # Image Normalization
+  normalize: True
+  normalizeScale: 1
+  # removeOutliers: None
+
+  # Resampling the image/mask
+  # resampledPixelSpacing: [1.00, 1.00, 1.00]
+  # interpolator: 'sitkBSpline'
+  # padDistance: 1
+
+  # Pre-Cropping
+  # preCrop: True
+  # Setting preCrop to true speeds up extraction and makes it less memory intensive, especially in the case of large images with only small ROIs.
+
+  # Resegmentation
+  # resegmentRange:
+  # resegmentMode: 'sigma'
+  # resegmentShape: True
+  # only first order and texture classes are calculated using the resegmented mask (known in IBSI as the intensity mask).
+
+  # Mask Validation
+  # minimunROIDimensions: 3
+  # 3D
+  # minimumROISize: 1
+  # geomertryTolerance: 1e-16
+  # correctMask: True
+
+  # Miscellaneous
+  # additionalInfo: True
+
+  # Feature Class Level
+  label: 3
+
+  # Image discretization
+  # bindWidth: 25
+
+  # Forced 2D extraction
+  force2D: False
+
+  # Texture matrix weighting
+  # weightingNorm: 'manhattan'
+  # only affects GLCM and GLRLM
+
+  # Distance to neighbour
+  # distances: [1]
+  # This only affects the GLCM and NGTDM feature classes. The GLSZM and GLRLM feature classes use a fixed distance of 1 (infinity norm) to define neighbours.
+
+  # Feature Class Specific Settings
+  # First Order
+  # voxelArrayShift: 0
+  # GLCM
+  # symmetricalGLCM: True
+  # GLDM
+  # gldm_a: 0
+
+  # Voxel-based specific settings
+  # kernelRadius: 1
+  # initValue: 0
+  # voxelBatch: 1
+  # Larger batches mean less loops in Python and therefore a quicker extraction, but do require more memory.