BUG: Fix incorrect check for minimum ROI dimensions.

By using `<=`, also ROIs that had the same number of dimensions as minimum dimensions were excluded.

Additionally, set the default value for required minimum dimensions to 2 (2D ROIs).

docs/customization.rst

@@ -201,7 +201,7 @@ Feature Extractor Level
 
 *Mask validation*
 
-- ``minimumROIDimensions`` [1]: Integer, range 1-3, specifies the minimum dimensions (1D, 2D or 3D, respectively).
+- ``minimumROIDimensions`` [2]: Integer, range 1-3, specifies the minimum dimensions (1D, 2D or 3D, respectively).
   Single-voxel segmentations are always excluded.
 - ``minimumROISize`` [None]: Integer, > 0, specifies the minimum number of voxels required. Test is skipped
   if this parameter is omitted (specifying it as None in the parameter file will throw an error).

radiomics/featureextractor.py

@@ -83,7 +83,7 @@ def _getDefaultSettings(cls):
     are defined in the respective feature classes and and not included here. Similarly, filter specific settings are
     defined in ``imageoperations.py`` and also not included here.
     """
-    return {'minimumROIDimensions': 1,
+    return {'minimumROIDimensions': 2,
             'minimumROISize': None,  # Skip testing the ROI size by default
             'normalize': False,
             'normalizeScale': 1,

radiomics/imageoperations.py

@@ -159,7 +159,7 @@ def checkMask(imageNode, maskNode, **kwargs):
   correctedMask = None
 
   label = kwargs.get('label', 1)
-  minDims = kwargs.get('minimumROIDimensions', 1)
+  minDims = kwargs.get('minimumROIDimensions', 2)
   minSize = kwargs.get('minimumROISize', None)
 
   logger.debug('Checking mask with label %d', label)
@@ -208,7 +208,7 @@ def checkMask(imageNode, maskNode, **kwargs):
 
   logger.debug('Checking minimum number of dimensions requirements (%d)', minDims)
   ndims = numpy.sum((boundingBox[1::2] - boundingBox[0::2] + 1) > 1)  # UBound - LBound + 1 = Size
-  if ndims <= minDims:
+  if ndims < minDims:
     logger.error('mask has too few dimensions (number of dimensions %d, minimum required %d)', ndims, minDims)
     return None, correctedMask