BUG: Fixed logic bugs in computing the candidateRegion for Caudate.

matsuij · Jan 15, 2013 · e165eb8 · e165eb8
1 parent 2446b94
commit e165eb8
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Showing 2 changed files with 10 additions and 5 deletions.
diff --git a/AutoWorkup/PipeLineFunctionHelpers.py b/AutoWorkup/PipeLineFunctionHelpers.py
@@ -19,7 +19,7 @@
 def convertToList(element):
     return [ element ]
 
-def MakeInclusionMaskForGMStructures( posteriorDictionary ):
+def MakeInclusionMaskForGMStructures( posteriorDictionary, candidateRegionFileName ):
     import SimpleITK as sitk
 
     AIR_FN=posteriorDictionary['AIR']
@@ -38,8 +38,12 @@ def MakeInclusionMaskForGMStructures( posteriorDictionary ):
     WM_Region=sitk.BinaryThreshold(WM_PROB,0.99,1.01,1,0) #NOTE: Higher tolerance for WM regions!
 
     outputCandidateRegion=sitk.BinaryThreshold(AIR_Region+CSF_Region+VB_Region+WM_Region,1,100,0,1) #NOTE: Inversion of input/output definitions
+    ##  Now write out the candidate region name.
+    import os
+    outputCandidateRegionFileName=os.path.realpath(candidateRegionFileName)
+    sitk.WriteImage(outputCandidateRegion,outputCandidateRegionFileName)
 
-    return outputCandidateRegion
+    return outputCandidateRegionFileName
 
 def makeListOfValidImages(imageFile):
     if imageFile is None:

diff --git a/AutoWorkup/WorkupT1T2BRAINSCut.py b/AutoWorkup/WorkupT1T2BRAINSCut.py
@@ -198,11 +198,12 @@ def CreateBRAINSCutWorkflow(projectid,
     cutWF.connect(inputsSpec, 'T1Volume', RF12BC, 'inputSubjectT1Filename')
 
     from PipeLineFunctionHelpers import MakeInclusionMaskForGMStructures;
-    makeCandidateRegionNode = pe.Node(interface=Function(['posteriorDictionary'],
-                                                    ['outputCandidateRegion'],
+    makeCandidateRegionNode = pe.Node(interface=Function(['posteriorDictionary','candidateRegionFileName'],
+                                                    ['outputCandidateRegionFileName'],
                                                     function=MakeInclusionMaskForGMStructures), name="MakeCandidateRegion")
+    makeCandidateRegionNode.inputs.candidateRegionFileName = "RF12_CandidateRegionMask.nii.gz"
     cutWF.connect(inputsSpec,'posteriorDictionary',makeCandidateRegionNode,'posteriorDictionary')
-    cutWF.connect(makeCandidateRegionNode,'outputCandidateRegion', RF12BC,'candidateRegion')
+    cutWF.connect(makeCandidateRegionNode,'outputCandidateRegionFileName', RF12BC,'candidateRegion')
 
     if not t1Only:
         cutWF.connect(inputsSpec, 'T2Volume', RF12BC, 'inputSubjectT2Filename')