Merge pull request AIM-Harvard#1 from rcuocolo/rcuocolo-2D-example

Example of 2D extraction from MRI images.

examples/exampleSettings/MR_2D_extraction.yaml

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+# This is an example of settings that can be used as a starting point for extractting 2D features from MR data 
+# This is only intended as a starting point and is not likely to be the optimal settings for your dataset.
+# Some points in determining better values are added as comments where appropriate
+
+# When adapting and using these settings for an analysis, be sure to add the PyRadiomics version used to allow you to
+# easily recreate your extraction at a later timepoint:
+
+# #############################  Extracted using PyRadiomics version: <version>  ######################################
+
+imageType:
+  Original: {}
+  LoG:
+    sigma: [2.0, 3.0, 4.0, 5.0]
+  Wavelet: {}
+
+featureClass:
+  shape2D:
+  firstorder:
+  glcm:
+    - 'Autocorrelation'
+    - 'JointAverage'
+    - 'ClusterProminence'
+    - 'ClusterShade'
+    - 'ClusterTendency'
+    - 'Contrast'
+    - 'Correlation'
+    - 'DifferenceAverage'
+    - 'DifferenceEntropy'
+    - 'DifferenceVariance'
+    - 'JointEnergy'
+    - 'JointEntropy'
+    - 'Imc1'
+    - 'Imc2'
+    - 'Idm'
+    - 'Idmn'
+    - 'Id'
+    - 'Idn'
+    - 'InverseVariance'
+    - 'MaximumProbability'
+    - 'SumEntropy'
+    - 'SumSquares'
+  glrlm:
+  glszm:
+  gldm:
+
+setting:
+  # Normalization:
+  normalize: true
+  normalizeScale: 100  # This allows you to use more or less the same bin width.
+
+  # Resampling:
+  interpolator: 'sitkBSpline'
+  resampledPixelSpacing: [2, 2, 0] # first dimensions always correspond to in-plane resolution. Z-plane resolution should not be modified to avoid mask errors (> than 1 slice after resampling)
+  padDistance: 10  # Extra padding for large sigma valued LoG filtered images
+  preCrop: true
+
+
+  # 2D settings
+  # force2Ddimension setting is relative to the acquisition plane. For example, the axial plane (0) corresponds to the acquisition plane (axial, sagittal or coronal) of the MRI volume.
+  # Therefore, in most cases this setting should not be modified as the axial plane has the best resolution on the original images and is of greater interest.
+  force2DDimension: 0
+
+  # Image discretization:
+  binWidth: 5
+
+  # first order specific settings:
+  # When normalizing, gray values below the mean will be negative. Shifting by 300 (3 StdDevs * 100) ensures that the
+  # majority of voxels is positive (only outliers >3 SD lower than the mean will be negative).
+  voxelArrayShift: 300
+
+  # Misc:
+  # default label value. Labels can also be defined in the call to featureextractor.execute, as a commandline argument,
+  # or in a column "Label" in the input csv (batchprocessing)
+  label: 1