diff --git a/AutoWorkup/WorkupT1T2BRAINSCut.py b/AutoWorkup/WorkupT1T2BRAINSCut.py index 34ddfecb..199d5106 100644 --- a/AutoWorkup/WorkupT1T2BRAINSCut.py +++ b/AutoWorkup/WorkupT1T2BRAINSCut.py @@ -182,23 +182,37 @@ def CreateBRAINSCutWorkflow(projectid, 'posteriorDictionary', 'RegistrationROI', 'atlasToSubjectTransform']), name='inputspec') + """ + Denoised T1 input for BRAINSCut + """ + denosingTimeStep=0.0625 + denosingConductance=0.4 + denosingIteration=5 - if not t1Only: - """ - Denoised input for BRAINSCut - """ - denosingTimeStep=0.0625 - denosingConductance=0.4 - denosingIteration=5 + DenoisedT1 = pe.Node(interface=GradientAnisotropicDiffusionImageFilter(), name="DenoisedT1") + DenoisedT1.inputs.timeStep = denosingTimeStep + DenoisedT1.inputs.conductance = denosingConductance + DenoisedT1.inputs.numberOfIterations = denosingIteration + DenoisedT1.inputs.outputVolume = "DenoisedT1.nii.gz" + + cutWF.connect(inputsSpec, 'T1Volume', DenoisedT1, 'inputVolume') + + """ + Gradient Anistropic Diffusion T1 images for BRAINSCut + """ + GADT1 = pe.Node(interface=GradientAnisotropicDiffusionImageFilter(), name="GADT1") + GADT1.inputs.timeStep = 0.025 + GADT1.inputs.conductance = 1 + GADT1.inputs.numberOfIterations = 5 + GADT1.inputs.outputVolume = "GADT1.nii.gz" - DenoisedT1 = pe.Node(interface=GradientAnisotropicDiffusionImageFilter(), name="DenoisedT1") - DenoisedT1.inputs.timeStep = denosingTimeStep - DenoisedT1.inputs.conductance = denosingConductance - DenoisedT1.inputs.numberOfIterations = denosingIteration - DenoisedT1.inputs.outputVolume = "DenoisedT1.nii.gz" + cutWF.connect(inputsSpec, 'T1Volume', GADT1, 'inputVolume') - cutWF.connect(inputsSpec, 'T1Volume', DenoisedT1, 'inputVolume') + if not t1Only: + """ + Denoised T1 input for BRAINSCut + """ DenoisedT2 = pe.Node(interface=GradientAnisotropicDiffusionImageFilter(), name="DenoisedT2") DenoisedT2.inputs.timeStep = denosingTimeStep DenoisedT2.inputs.conductance = denosingConductance @@ -208,16 +222,8 @@ def CreateBRAINSCutWorkflow(projectid, cutWF.connect(inputsSpec, 'T2Volume', DenoisedT2, 'inputVolume') """ - Gradient Anistropic Diffusion images for BRAINSCut + Gradient Anistropic Diffusion T1 images for BRAINSCut """ - GADT1 = pe.Node(interface=GradientAnisotropicDiffusionImageFilter(), name="GADT1") - GADT1.inputs.timeStep = 0.025 - GADT1.inputs.conductance = 1 - GADT1.inputs.numberOfIterations = 5 - GADT1.inputs.outputVolume = "GADT1.nii.gz" - - cutWF.connect(inputsSpec, 'T1Volume', GADT1, 'inputVolume') - GADT2 = pe.Node(interface=GradientAnisotropicDiffusionImageFilter(), name="GADT2") GADT2.inputs.timeStep = 0.025 GADT2.inputs.conductance = 1