registration.py

    fgm=slicer.modules.brainsroiauto
    fgmPar={}
    fgmPar["cropOutput"]=True
    fgmPar["inputVolume"]=movingImage
    fgmPar["outputVolume"]=movingImage
    slicer.cli.run(fgm, None, fgmPar, True)
  
    fgmPar["inputVolume"]=fixedImage
    fgmPar["outputVolume"]=fixedImage
    slicer.cli.run(fgm, None, fgmPar, True)

    #the above is NOT equivalent to reg1params["maskProcessingMode"]="ROIAUTO"
    reg1params={}
    reg1params["initializeTransformMode"] = "useMomentsAlign"
    reg1params["samplingPercentage"] = 0.02
    reg1params["numberOfHistogramBins"] = 20
    reg1params["translationScale"] = 5000
    reg1params["fixedVolume"] = fixedImage
    reg1params["movingVolume"] = movingImage
    reg1params["transformType"] = "Rigid"
    reg = slicer.mrmlScene.CreateNodeByClass("vtkMRMLLinearTransformNode")
    reg.SetName("imageRegistrationTransform")
    reg1params["linearTransform"] = reg
    slicer.mrmlScene.AddNode(reg)
    slicer.cli.run(slicer.modules.brainsfit, None, reg1params, wait_for_completion = True)