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Purpose

The purpose of this pipeline is to complete all the pre-processing steps needed to turn diffusion-weighted images into FA images that will be used to build a template diffusion tensor atlas for fiber tracking.

Inputs

The input to this pipeline is a list of subject IDs that is used to generate lists of the corresponding DWIs processed with automated quality control, T2s, and brain label images that are treated as brain masks.

Pipeline Steps for CreateDWIWorkflow

{Fill this part later}





In [36]:



    


## Boiler plate code common to many notebooks.  See the TestFilesCommonCode.ipynb for details
#from __future__ import print_function
#%run TestFilesCommonCode.ipynb



    











In [1]:



    


import os
import glob
import sys

#\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/
#####################################################################################
#     Prepend the shell environment search paths
PROGRAM_PATHS = '/scratch/NAMICExternalProjects/release/bin'
PROGRAM_PATHS = PROGRAM_PATHS.split(':')
PROGRAM_PATHS.extend(os.environ['PATH'].split(':'))
os.environ['PATH'] = ':'.join(PROGRAM_PATHS)

CUSTOM_ENVIRONMENT=dict()

# Platform specific information
#     Prepend the python search paths
PYTHON_AUX_PATHS = '/scratch/NAMICExternalProjects/release/BRAINSTools/AutoWorkup'
PYTHON_AUX_PATHS = PYTHON_AUX_PATHS.split(':')
PYTHON_AUX_PATHS.extend(sys.path)
sys.path = PYTHON_AUX_PATHS

import SimpleITK as sitk
import nipype
from nipype.interfaces import ants
from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec, File, Directory
from nipype.interfaces.base import traits, isdefined, BaseInterface
from nipype.interfaces.utility import Merge, Split, Function, Rename, IdentityInterface
import nipype.interfaces.io as nio   # Data i/oS
import nipype.pipeline.engine as pe  # pypeline engine
from nipype.interfaces.freesurfer import ReconAll
from SEMTools import *



    











In [11]:



    


######## Input scans #############################
DWI_scan = '/Shared/johnsonhj/TrackOn/Experiments/20140203_DWIProcessing/VISUALLY_INSPECTED/HDNI_003/823955340/823955340_20080609_30/823955340_823955340_20080609_30_DWI_CONCAT_QCed_INSPECTED.nrrd'

sessionID = os.path.basename(os.path.dirname(DWI_scan))
subjectID = os.path.basename(os.path.dirname(os.path.dirname(DWI_scan)))
siteID = os.path.basename(os.path.dirname(os.path.dirname(os.path.dirname(DWI_scan))))

scalarsDIR = os.path.join('/Shared/sinapse/CACHE/20141124_TrackOn_base_Results/',
                          siteID,
                          subjectID,
                          sessionID,
                          'TissueClassify')

T2_scan = os.path.join(scalarsDIR,'t2_average_BRAINSABC.nii.gz')
labelMap_image = os.path.join(scalarsDIR,'complete_brainlabels_seg.nii.gz')
#################################################

####### Workflow ################################
WFname = 'DWIWorkflow_' + sessionID
DWIWorkflow = pe.Workflow(name=WFname)
BASE_DIR = os.path.join('/scratch/TESTS/IpythonNotebook', '1_DWI_Nipype_workflow')
DWIWorkflow.base_dir = BASE_DIR

inputsSpec = pe.Node(interface=IdentityInterface(fields=['T2Volume', 'DWIVolume','LabelMapVolume']), 
                     name='inputspec')

inputsSpec.inputs.DWIVolume = DWI_scan
inputsSpec.inputs.T2Volume = T2_scan
inputsSpec.inputs.LabelMapVolume = labelMap_image

outputsSpec = pe.Node(interface=IdentityInterface(fields=['CorrectedDWI_in_T2Space','tensor_image','DWIBrainMask',
                                                          'FAImage','MDImage','RDImage','FrobeniusNormImage',
                                                          'Lambda1Image','Lambda2Image','Lambda3Image']),
                      name='outputsSpec')

# Step0: remove the skull from the T2 volume
def ExtractBRAINFromHead(RawScan, BrainLabels):
    import os
    import SimpleITK as sitk
    # Remove skull from the head scan
    assert os.path.exists(RawScan), "File not found: %s" % RawScan
    assert os.path.exists(BrainLabels), "File not found: %s" % BrainLabels
    headImage = sitk.ReadImage(RawScan)
    labelsMap = sitk.ReadImage(BrainLabels)
    label_mask = labelsMap>0
    brainImage = sitk.Cast(headImage,sitk.sitkInt16) * sitk.Cast(label_mask,sitk.sitkInt16)
    outputVolume = os.path.realpath('T2Stripped.nrrd')
    sitk.WriteImage(brainImage, outputVolume)
    return outputVolume

ExtractBRAINFromHeadNode = pe.Node(interface=Function(function = ExtractBRAINFromHead, 
                                                      input_names=['RawScan','BrainLabels'],
                                                      output_names=['outputVolume']), 
                                   name="ExtractBRAINFromHead")

DWIWorkflow.connect(inputsSpec, 'T2Volume', ExtractBRAINFromHeadNode, 'RawScan')
DWIWorkflow.connect(inputsSpec, 'LabelMapVolume', ExtractBRAINFromHeadNode, 'BrainLabels')

# Step1: extract B0 from DWI volume
EXTRACT_B0 = pe.Node(interface=extractNrrdVectorIndex(),name="EXTRACT_B0")
EXTRACT_B0.inputs.vectorIndex = 0
EXTRACT_B0.inputs.outputVolume = 'B0_Image.nrrd'
DWIWorkflow.connect(inputsSpec,'DWIVolume',EXTRACT_B0,'inputVolume')

# Step2: Register T2 to B0 space using BRAINSFit
BFit_T2toB0 = pe.Node(interface=BRAINSFit(), name="BFit_T2toB0")
BFit_T2toB0.inputs.costMetric = "MMI"
BFit_T2toB0.inputs.numberOfSamples = 100000
BFit_T2toB0.inputs.numberOfIterations = [1500]
BFit_T2toB0.inputs.numberOfHistogramBins = 50
BFit_T2toB0.inputs.maximumStepLength = 0.2
BFit_T2toB0.inputs.minimumStepLength = [0.00005]
BFit_T2toB0.inputs.useRigid = True
BFit_T2toB0.inputs.useAffine = True
BFit_T2toB0.inputs.maskInferiorCutOffFromCenter = 65
BFit_T2toB0.inputs.maskProcessingMode = "ROIAUTO"
BFit_T2toB0.inputs.ROIAutoDilateSize = 13
BFit_T2toB0.inputs.backgroundFillValue = 0.0
BFit_T2toB0.inputs.initializeTransformMode = 'useCenterOfHeadAlign'
BFit_T2toB0.inputs.strippedOutputTransform = "T2ToB0_RigidTransform.h5"
#BFit_T2toB0.inputs.outputVolume = "T2_in_B0Space_Output.nii.gz"
DWIWorkflow.connect(EXTRACT_B0, 'outputVolume', BFit_T2toB0, 'fixedVolume')
DWIWorkflow.connect(ExtractBRAINFromHeadNode, 'outputVolume', BFit_T2toB0, 'movingVolume')

# Step3: Use T_rigid to "resample" T2 and label map images to B0 image space
#------------
def MakeResamplerInFileList(inputT2, inputLabelMap):
    imagesList = [inputT2, inputLabelMap]
    return imagesList
    
MakeResamplerInFilesListNode = pe.Node(Function(function=MakeResamplerInFileList,
                                               input_names=['inputT2','inputLabelMap'],
                                               output_names=['imagesList']),
                                      name="MakeResamplerInFilesListNode")

DWIWorkflow.connect([(ExtractBRAINFromHeadNode,MakeResamplerInFilesListNode,[('outputVolume','inputT2')]),
                     (inputsSpec,MakeResamplerInFilesListNode,[('LabelMapVolume','inputLabelMap')])])

ResampleToB0Space = pe.MapNode(interface=BRAINSResample(), name="ResampleToB0Space",
                               iterfield=['inputVolume', 'pixelType', 'outputVolume'])
ResampleToB0Space.inputs.interpolationMode = 'Linear'
ResampleToB0Space.inputs.outputVolume = ['T2toB0.nrrd','BRAINMaskToB0.nrrd']
ResampleToB0Space.inputs.pixelType = ['ushort','binary']
DWIWorkflow.connect(BFit_T2toB0,'strippedOutputTransform',ResampleToB0Space,'warpTransform')
DWIWorkflow.connect(EXTRACT_B0,'outputVolume',ResampleToB0Space,'referenceVolume')
DWIWorkflow.connect(MakeResamplerInFilesListNode,'imagesList',ResampleToB0Space,'inputVolume')

# This function helps to pick desirable output from the outputVolume list
def pickFromList(inlist,item):
    return inlist[item]

# Step4: Create registration mask from resampled label map image
def CreateAntsRegistrationMask(brainMask):
    import os
    import SimpleITK as sitk
    assert os.path.exists(brainMask), "File not found: %s" % brainMask
    labelsMap = sitk.ReadImage(brainMask)
    label_mask = labelsMap>0
    # erode the label mask
    erodeFilter = sitk.BinaryErodeImageFilter()
    erodeFilter.SetKernelRadius(4)
    eroded_mask = erodeFilter.Execute( label_mask )
    # dilate the label mask
    dilateFilter = sitk.BinaryDilateImageFilter()
    dilateFilter.SetKernelRadius(4)
    dilated_mask = dilateFilter.Execute( label_mask )
    regMask = eroded_mask - dilated_mask
    registrationMask = os.path.realpath('registrationMask.nrrd')
    sitk.WriteImage(regMask, registrationMask)
    return registrationMask
    
CreateRegistrationMask = pe.Node(interface=Function(function = CreateAntsRegistrationMask, 
                                                    input_names=['brainMask'],
                                                    output_names=['registrationMask']),
                                 name="CreateAntsRegistrationMask")

DWIWorkflow.connect(ResampleToB0Space, ('outputVolume', pickFromList, 1), 
                    CreateRegistrationMask, 'brainMask')

# Step5: Save direction cosine for the resampled T2 image
def SaveDirectionCosineToMatrix(inputVolume):
    import os
    import SimpleITK as sitk
    assert os.path.exists(inputVolume), "File not found: %s" % inputVolume
    t2 = sitk.ReadImage(inputVolume)
    directionCosine = t2.GetDirection()
    return directionCosine

SaveDirectionCosineToMatrixNode = pe.Node(interface=Function(function = SaveDirectionCosineToMatrix, 
                                                             input_names=['inputVolume'],
                                                             output_names=['directionCosine']),
                                          name="SaveDirectionCosineToMatrix")

DWIWorkflow.connect(ResampleToB0Space, ('outputVolume', pickFromList, 0), 
                    SaveDirectionCosineToMatrixNode, 'inputVolume')

# Step6: Force DC to ID
def MakeForceDCFilesList(inputB0, inputT2, inputLabelMap):
    import os
    assert os.path.exists(inputB0), "File not found: %s" % inputB0
    assert os.path.exists(inputT2), "File not found: %s" % inputT2
    assert os.path.exists(inputLabelMap), "File not found: %s" % inputLabelMap
    imagesList = [inputB0, inputT2, inputLabelMap]
    return imagesList
    
MakeForceDCFilesListNode = pe.Node(Function(function=MakeForceDCFilesList,
                                             input_names=['inputB0','inputT2','inputLabelMap'],
                                             output_names=['imagesList']),
                                    name="MakeForceDCFilesListNode")


DWIWorkflow.connect([(EXTRACT_B0,MakeForceDCFilesListNode,[('outputVolume','inputB0')]),
                     (ResampleToB0Space,MakeForceDCFilesListNode,[(('outputVolume', pickFromList, 0),'inputT2')]),
                     (CreateRegistrationMask,MakeForceDCFilesListNode,[('registrationMask','inputLabelMap')])])

def ForceDCtoID(inputVolume):
    import os
    import SimpleITK as sitk
    inImage = sitk.ReadImage(inputVolume)
    inImage.SetDirection((1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0))
    outputVolume = os.path.realpath('IDDC_'+ os.path.basename(inputVolume))
    sitk.WriteImage(inImage, outputVolume)
    return outputVolume

ForceDCtoIDNode = pe.MapNode(interface=Function(function = ForceDCtoID, 
                                                input_names=['inputVolume'],
                                                output_names=['outputVolume']), 
                             name="ForceDCtoID",
                             iterfield=['inputVolume'])

DWIWorkflow.connect(MakeForceDCFilesListNode, 'imagesList', ForceDCtoIDNode, 'inputVolume')

# Step7: Run antsRegistration in one direction
antsReg_B0ToTransformedT2 = pe.Node(interface=ants.Registration(), name="antsReg_B0ToTransformedT2")
antsReg_B0ToTransformedT2.inputs.dimension = 3
antsReg_B0ToTransformedT2.inputs.transforms = ["SyN"]
antsReg_B0ToTransformedT2.inputs.transform_parameters = [(0.25, 3.0, 0.0)]
antsReg_B0ToTransformedT2.inputs.metric = ['MI']
antsReg_B0ToTransformedT2.inputs.sampling_strategy = [None]
antsReg_B0ToTransformedT2.inputs.sampling_percentage = [1.0]
antsReg_B0ToTransformedT2.inputs.metric_weight = [1.0]
antsReg_B0ToTransformedT2.inputs.radius_or_number_of_bins = [32]
antsReg_B0ToTransformedT2.inputs.number_of_iterations = [[70, 50, 40]]
antsReg_B0ToTransformedT2.inputs.convergence_threshold = [1e-6]
antsReg_B0ToTransformedT2.inputs.convergence_window_size = [10]
antsReg_B0ToTransformedT2.inputs.use_histogram_matching = [True]
antsReg_B0ToTransformedT2.inputs.shrink_factors = [[3, 2, 1]]
antsReg_B0ToTransformedT2.inputs.smoothing_sigmas = [[2, 1, 0]]
antsReg_B0ToTransformedT2.inputs.sigma_units = ["vox"]
antsReg_B0ToTransformedT2.inputs.use_estimate_learning_rate_once = [False]
antsReg_B0ToTransformedT2.inputs.write_composite_transform = True
antsReg_B0ToTransformedT2.inputs.collapse_output_transforms = False
antsReg_B0ToTransformedT2.inputs.initialize_transforms_per_stage = False
antsReg_B0ToTransformedT2.inputs.output_transform_prefix = 'Tsyn'
antsReg_B0ToTransformedT2.inputs.winsorize_lower_quantile = 0.01
antsReg_B0ToTransformedT2.inputs.winsorize_upper_quantile = 0.99
antsReg_B0ToTransformedT2.inputs.args = '--float 1 --restrict-deformation 0x1x0'

DWIWorkflow.connect(ForceDCtoIDNode, ('outputVolume', pickFromList, 1), antsReg_B0ToTransformedT2, 'fixed_image')
DWIWorkflow.connect(ForceDCtoIDNode, ('outputVolume', pickFromList, 2), antsReg_B0ToTransformedT2, 'fixed_image_mask')
DWIWorkflow.connect(ForceDCtoIDNode, ('outputVolume', pickFromList, 0), antsReg_B0ToTransformedT2, 'moving_image')

# Step8: Now, all necessary transforms are acquired. It's a time to 
#        transform input DWI image into T2 image space
# {DWI} --> ForceDCtoID --> gtractResampleDWIInPlace(using SyN transfrom) 
# --> Restore DirectionCosine From Saved Matrix --> gtractResampleDWIInPlace(inverse of T_rigid from BFit)
# --> {CorrectedDW_in_T2Space}

DWI_ForceDCtoIDNode = pe.Node(interface=Function(function = ForceDCtoID, 
                                                 input_names=['inputVolume'],
                                                 output_names=['outputVolume']), 
                              name='DWI_ForceDCtoIDNode')

DWIWorkflow.connect(inputsSpec,'DWIVolume',DWI_ForceDCtoIDNode,'inputVolume')

def pickCompositeTransfromFromList(composite_transform_as_list):
    return composite_transform_as_list[0]

gtractResampleDWI_SyN = pe.Node(interface=gtractResampleDWIInPlace(), 
                                       name="gtractResampleDWI_SyN")

DWIWorkflow.connect(DWI_ForceDCtoIDNode,'outputVolume',gtractResampleDWI_SyN,'inputVolume')
DWIWorkflow.connect(antsReg_B0ToTransformedT2,('composite_transform',pickCompositeTransfromFromList),gtractResampleDWI_SyN,'warpDWITransform')
DWIWorkflow.connect(ForceDCtoIDNode,('outputVolume', pickFromList, 1),gtractResampleDWI_SyN,'referenceVolume') # fixed image of antsRegistration
gtractResampleDWI_SyN.inputs.outputVolume = 'IDDC_correctedDWI.nrrd'

def RestoreDCFromSavedMatrix(inputVolume, inputDirectionCosine):
    import os
    import SimpleITK as sitk
    inImage = sitk.ReadImage(inputVolume)
    inImage.SetDirection(inputDirectionCosine)
    outputVolume = os.path.realpath('correctedDWI.nrrd')
    sitk.WriteImage(inImage, outputVolume)
    return outputVolume

RestoreDCFromSavedMatrixNode = pe.Node(interface=Function(function = RestoreDCFromSavedMatrix, 
                                                          input_names=['inputVolume','inputDirectionCosine'],
                                                          output_names=['outputVolume']), 
                                       name='RestoreDCFromSavedMatrix')

DWIWorkflow.connect(gtractResampleDWI_SyN,'outputVolume',RestoreDCFromSavedMatrixNode,'inputVolume')
DWIWorkflow.connect(SaveDirectionCosineToMatrixNode,'directionCosine',RestoreDCFromSavedMatrixNode,'inputDirectionCosine')

def GetRigidTransformInverse(inputTransform):
    import os
    import SimpleITK as sitk
    inputTx = sitk.ReadTransform(inputTransform)
    versorRigidTx = sitk.VersorRigid3DTransform()
    versorRigidTx.SetFixedParameters(inputTx.GetFixedParameters())
    versorRigidTx.SetParameters(inputTx.GetParameters())
    invTx = versorRigidTx.GetInverse()
    inverseTransform = os.path.realpath('Inverse_'+ os.path.basename(inputTransform))
    sitk.WriteTransform(invTx, inverseTransform)
    return inverseTransform

GetRigidTransformInverseNode = pe.Node(interface=Function(function = GetRigidTransformInverse, 
                                                          input_names=['inputTransform'],
                                                          output_names=['inverseTransform']), 
                                       name='GetRigidTransformInverse')

DWIWorkflow.connect(BFit_T2toB0,'strippedOutputTransform',GetRigidTransformInverseNode,'inputTransform')

gtractResampleDWIInPlace_Trigid = pe.Node(interface=gtractResampleDWIInPlace(), 
                                       name="gtractResampleDWIInPlace_Trigid")

DWIWorkflow.connect(RestoreDCFromSavedMatrixNode,'outputVolume',gtractResampleDWIInPlace_Trigid,'inputVolume')
DWIWorkflow.connect(GetRigidTransformInverseNode,'inverseTransform',gtractResampleDWIInPlace_Trigid,'inputTransform') #Inverse of rigid transform from BFit
gtractResampleDWIInPlace_Trigid.inputs.outputVolume = 'CorrectedDWI_in_T2Space.nrrd'
gtractResampleDWIInPlace_Trigid.inputs.outputResampledB0 = 'CorrectedDWI_in_T2Space_B0.nrrd'

# Finally we pass the outputs of the gtractResampleDWIInPlace_Trigid to the outputsSpec
DWIWorkflow.connect(gtractResampleDWIInPlace_Trigid, 'outputVolume', outputsSpec, 'CorrectedDWI_in_T2Space')

# Step9: Create brain mask from the input labelmap
DWIBRAINMASK = pe.Node(interface=BRAINSResample(), name='DWIBRAINMASK')
DWIBRAINMASK.inputs.interpolationMode = 'Linear'
DWIBRAINMASK.inputs.outputVolume = 'BrainMaskForDWI.nrrd'
DWIBRAINMASK.inputs.pixelType = 'binary'
DWIWorkflow.connect(gtractResampleDWIInPlace_Trigid,'outputResampledB0',DWIBRAINMASK,'referenceVolume')
DWIWorkflow.connect(inputsSpec,'LabelMapVolume',DWIBRAINMASK,'inputVolume')
DWIWorkflow.connect(DWIBRAINMASK, 'outputVolume', outputsSpec, 'DWIBrainMask')

# Step10: DTI estimation
DTIEstim = pe.Node(interface=dtiestim(), name="DTIEstim")
DTIEstim.inputs.method = 'wls'
DTIEstim.inputs.tensor_output = 'DTI_Output.nrrd'
DWIWorkflow.connect(gtractResampleDWIInPlace_Trigid, 'outputVolume', DTIEstim, 'dwi_image')
DWIWorkflow.connect(DWIBRAINMASK, 'outputVolume', DTIEstim, 'brain_mask')
DWIWorkflow.connect(DTIEstim, 'tensor_output', outputsSpec, 'tensor_image')

# Step11: DTI process
DTIProcess = pe.Node(interface=dtiprocess(), name='DTIProcess')
DTIProcess.inputs.fa_output = 'FA.nrrd'
DTIProcess.inputs.md_output = 'MD.nrrd'
DTIProcess.inputs.RD_output = 'RD.nrrd'
DTIProcess.inputs.frobenius_norm_output = 'frobenius_norm_output.nrrd'
DTIProcess.inputs.lambda1_output = 'lambda1_output.nrrd'
DTIProcess.inputs.lambda2_output = 'lambda2_output.nrrd'
DTIProcess.inputs.lambda3_output = 'lambda3_output.nrrd'
DTIProcess.inputs.scalar_float = True

DWIWorkflow.connect(DTIEstim, 'tensor_output', DTIProcess, 'dti_image')
DWIWorkflow.connect(DTIProcess, 'fa_output', outputsSpec, 'FAImage')
DWIWorkflow.connect(DTIProcess, 'md_output', outputsSpec, 'MDImage')
DWIWorkflow.connect(DTIProcess, 'RD_output', outputsSpec, 'RDImage')
DWIWorkflow.connect(DTIProcess, 'frobenius_norm_output', outputsSpec, 'FrobeniusNormImage')
DWIWorkflow.connect(DTIProcess, 'lambda1_output', outputsSpec, 'Lambda1Image')
DWIWorkflow.connect(DTIProcess, 'lambda2_output', outputsSpec, 'Lambda2Image')
DWIWorkflow.connect(DTIProcess, 'lambda3_output', outputsSpec, 'Lambda3Image')

# Step12: Write outputs with DataSink 
DWIDataSink = pe.Node(interface=nio.DataSink(), name='DWIDataSink')
DWIDataSink.inputs.base_directory = os.path.join(BASE_DIR,'Results')
DWIDataSink.inputs.container = sessionID

DWIWorkflow.connect(outputsSpec, 'CorrectedDWI_in_T2Space', DWIDataSink, 'Outputs.@CorrectedDWI_in_T2Space')
DWIWorkflow.connect(outputsSpec, 'tensor_image', DWIDataSink, 'Outputs.@tensor_image')
DWIWorkflow.connect(outputsSpec, 'DWIBrainMask', DWIDataSink, 'Outputs.@DWIBrainMask')
DWIWorkflow.connect(outputsSpec, 'FAImage', DWIDataSink, 'Outputs.@FAImage')
DWIWorkflow.connect(outputsSpec, 'MDImage', DWIDataSink, 'Outputs.@MDImage')
DWIWorkflow.connect(outputsSpec, 'RDImage', DWIDataSink, 'Outputs.@RDImage')
DWIWorkflow.connect(outputsSpec, 'FrobeniusNormImage', DWIDataSink, 'Outputs.@FrobeniusNormImage')
DWIWorkflow.connect(outputsSpec, 'Lambda1Image', DWIDataSink, 'Outputs.@Lambda1Image')
DWIWorkflow.connect(outputsSpec, 'Lambda2Image', DWIDataSink, 'Outputs.@Lambda2Image')
DWIWorkflow.connect(outputsSpec, 'Lambda3Image', DWIDataSink, 'Outputs.@Lambda3Image')

DWIWorkflow.write_graph()
DWIWorkflow.run()



    


















    






INFO:workflow:Converting dotfile: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/graph.dot to png format
INFO:workflow:['check', 'execution', 'logging']
INFO:workflow:Running serially.
INFO:workflow:Executing node EXTRACT_B0 in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/EXTRACT_B0
INFO:workflow:Running:  extractNrrdVectorIndex  --inputVolume /Shared/johnsonhj/TrackOn/Experiments/20140203_DWIProcessing/VISUALLY_INSPECTED/HDNI_003/823955340/823955340_20080609_30/823955340_823955340_20080609_30_DWI_CONCAT_QCed_INSPECTED.nrrd --outputVolume B0_Image.nrrd --vectorIndex 0
INFO:interface:stdout 2015-01-11T20:53:03.515318:Input Image: /Shared/johnsonhj/TrackOn/Experiments/20140203_DWIProcessing/VISUALLY_INSPECTED/HDNI_003/823955340/823955340_20080609_30/823955340_823955340_20080609_30_DWI_CONCAT_QCed_INSPECTED.nrrd
INFO:interface:stdout 2015-01-11T20:53:03.515318:Output Image: B0_Image.nrrd
INFO:interface:stdout 2015-01-11T20:53:03.515318:Vector Index: 0
INFO:interface:stdout 2015-01-11T20:53:03.515318:Set Image Orientation: AsAcquired
INFO:interface:stdout 2015-01-11T20:53:03.515318:
INFO:workflow:Executing node DWI_ForceDCtoIDNode in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/DWI_ForceDCtoIDNode
INFO:workflow:Executing node ExtractBRAINFromHead in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ExtractBRAINFromHead
INFO:workflow:Executing node BFit_T2toB0 in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/BFit_T2toB0
INFO:workflow:Running:  BRAINSFit  --ROIAutoDilateSize 13.000000 --backgroundFillValue 0.000000 --costMetric MMI --fixedVolume /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/EXTRACT_B0/B0_Image.nrrd --initializeTransformMode useCenterOfHeadAlign --maskInferiorCutOffFromCenter 65.000000 --maskProcessingMode ROIAUTO --maximumStepLength 0.200000 --minimumStepLength 5e-05 --movingVolume /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ExtractBRAINFromHead/T2Stripped.nrrd --numberOfHistogramBins 50 --numberOfIterations 1500 --numberOfSamples 100000 --strippedOutputTransform T2ToB0_RigidTransform.h5 --useAffine  --useRigid 
INFO:interface:stdout 2015-01-11T20:53:05.102716:Original Fixed image origin[-109.009, -109.767, -56.6923, 0]
INFO:interface:stdout 2015-01-11T20:53:05.245322:ListSample TotalFrequency is  802816
INFO:interface:stdout 2015-01-11T20:53:05.320230:1057 ValidHistogramsEntries,  802816 TotalFrequency
INFO:interface:stdout 2015-01-11T20:53:05.320230:0.01 ---> 0
INFO:interface:stdout 2015-01-11T20:53:05.320230:0.99 ---> 401
INFO:interface:stdout 2015-01-11T20:53:05.350435:LowHigh Thresholds: [106,2147483647]
INFO:interface:stdout 2015-01-11T20:53:06.607667:ListSample TotalFrequency is  7990528
INFO:interface:stdout 2015-01-11T20:53:07.296193:4072 ValidHistogramsEntries,  7990528 TotalFrequency
INFO:interface:stdout 2015-01-11T20:53:07.296193:0.01 ---> 0
INFO:interface:stdout 2015-01-11T20:53:07.296193:0.99 ---> 2448
INFO:interface:stdout 2015-01-11T20:53:07.402275:LowHigh Thresholds: [752,2147483647]
INFO:interface:stdout 2015-01-11T20:53:19.933025:WARNING --numberOfSamples is deprecated, please use --samplingPercentage instead 
INFO:interface:stdout 2015-01-11T20:53:19.933025:WARNING: Replacing command line --samplingPercentage 0.124562
INFO:interface:stdout 2015-01-11T20:53:20.129343:TranformTypes: Rigid(1 of 2).
INFO:interface:stdout 2015-01-11T20:53:20.129343:
INFO:interface:stdout 2015-01-11T20:53:20.129343:TranformTypes: Affine(2 of 2).
INFO:interface:stdout 2015-01-11T20:53:20.129343:
INFO:interface:stdout 2015-01-11T20:53:20.129343:Initializing transform with useCenterOfHeadAlign
INFO:interface:stdout 2015-01-11T20:53:20.181794:maxSIDirection = 105.5
INFO:interface:stdout 2015-01-11T20:53:20.269115:Computing Sampled Distance Computations
INFO:interface:stdout 2015-01-11T20:53:21.333091:maxSIDirection = 74.8159
INFO:interface:stdout 2015-01-11T20:53:21.342797:Computing Sampled Distance Computations
INFO:interface:stdout 2015-01-11T20:53:23.012370:Initializing transform with useCenterOfHeadAlign to 
INFO:interface:stdout 2015-01-11T20:53:23.012370:VersorRigid3DTransform (0x7fa371609050)
INFO:interface:stdout 2015-01-11T20:53:23.012370:  RTTI typeinfo:   itk::VersorRigid3DTransform<double>
INFO:interface:stdout 2015-01-11T20:53:23.014387:  Reference Count: 2
INFO:interface:stdout 2015-01-11T20:53:23.014387:  Modified Time: 403160
INFO:interface:stdout 2015-01-11T20:53:23.014387:  Debug: Off
INFO:interface:stdout 2015-01-11T20:53:23.014387:  Object Name: 
INFO:interface:stdout 2015-01-11T20:53:23.014387:  Observers: 
INFO:interface:stdout 2015-01-11T20:53:23.014387:    none
INFO:interface:stdout 2015-01-11T20:53:23.014387:  Matrix: 
INFO:interface:stdout 2015-01-11T20:53:23.014387:    0.99863 0.0520493 -0.0054706 
INFO:interface:stdout 2015-01-11T20:53:23.014387:    -0.052336 0.993159 -0.104385 
INFO:interface:stdout 2015-01-11T20:53:23.014387:    4.33681e-19 0.104528 0.994522 
INFO:interface:stdout 2015-01-11T20:53:23.014387:  Offset: [4.51482, 31.5197, 10.8616]
INFO:interface:stdout 2015-01-11T20:53:23.014387:  Center: [-4.06168, -10.8725, 2.19632]
INFO:interface:stdout 2015-01-11T20:53:23.014387:  Translation: [3.94247, 31.5774, 9.71312]
INFO:interface:stdout 2015-01-11T20:53:23.014387:  Inverse: 
INFO:interface:stdout 2015-01-11T20:53:23.014387:    0.99863 -0.052336 4.33681e-19 
INFO:interface:stdout 2015-01-11T20:53:23.014387:    0.0520493 0.993159 0.104528 
INFO:interface:stdout 2015-01-11T20:53:23.014387:    -0.0054706 -0.104385 0.994522 
INFO:interface:stdout 2015-01-11T20:53:23.014387:  Singular: 0
INFO:interface:stdout 2015-01-11T20:53:23.014387:  Versor: [ 0.052318, -0.00137, -0.0261411, 0.998287 ]
INFO:interface:stdout 2015-01-11T20:53:23.014387:
INFO:interface:stdout 2015-01-11T20:53:23.014387:===============================================
INFO:interface:stderr 2015-01-11T20:53:23.022234:maskInferiorCutOffFromCenter is 65
INFO:interface:stdout 2015-01-11T20:53:23.110909:
INFO:interface:stdout 2015-01-11T20:53:23.110909:
INFO:interface:stdout 2015-01-11T20:53:23.110909:
INFO:interface:stdout 2015-01-11T20:53:23.110909:=============================== ITKv4 Registration: Starting Transform Estimations for Rigid(1 of 2).===============================
INFO:interface:stdout 2015-01-11T20:53:23.110909:
INFO:interface:stdout 2015-01-11T20:53:23.846204:   0    -0.439435   [ 0.0508733 -0.00106022 -0.0257416 4.01597 31.4327 9.59626 ]
INFO:interface:stdout 2015-01-11T20:53:23.895101:   1    -0.448909   [ 0.0494417 -0.000357934 -0.0247833 4.08746 31.2765 9.49398 ]
INFO:interface:stdout 2015-01-11T20:53:23.945701:   2    -0.457452   [ 0.0492232 2.29808e-05 -0.0250755 4.16082 31.1363 9.37161 ]
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INFO:interface:stdout 2015-01-11T20:53:25.908997:  45    -0.702846   [ 0.0670507 -0.000150859 -0.0176268 5.04669 26.7987 6.44352 ]
INFO:interface:stdout 2015-01-11T20:53:25.954907:  46    -0.702844   [ 0.0669904 -0.000186831 -0.0175188 5.04653 26.7989 6.44281 ]
INFO:interface:stdout 2015-01-11T20:53:26.001393:  47    -0.702846   [ 0.0670492 -0.00018147 -0.0175465 5.04686 26.7987 6.44292 ]
INFO:interface:stdout 2015-01-11T20:53:26.048256:  48    -0.702852   [ 0.0670134 -0.000179746 -0.0175339 5.04683 26.7989 6.44305 ]
INFO:interface:stdout 2015-01-11T20:53:26.091415:  49    -0.702852   [ 0.0670229 -0.000183595 -0.0175312 5.04699 26.7989 6.44316 ]
INFO:interface:stdout 2015-01-11T20:53:26.140827:  50    -0.702849   [ 0.0670049 -0.000179469 -0.0175326 5.04701 26.799 6.44332 ]
INFO:interface:stdout 2015-01-11T20:53:26.185310:  51    -0.702847   [ 0.0670228 -0.00018281 -0.0175329 5.04707 26.799 6.44328 ]
INFO:interface:stdout 2015-01-11T20:53:26.231964:Stop condition from optimizer.RegularStepGradientDescentOptimizerv4: Step too small after 52 iterations. Current step (4.88281e-05) is less than minimum step (5e-05).
INFO:interface:stdout 2015-01-11T20:53:26.232768:
INFO:interface:stdout 2015-01-11T20:53:26.232768:
INFO:interface:stdout 2015-01-11T20:53:26.232768:
INFO:interface:stdout 2015-01-11T20:53:26.232768:=============================== ITKv4 Registration: Starting Transform Estimations for Affine(2 of 2).===============================
INFO:interface:stdout 2015-01-11T20:53:26.232768:
INFO:interface:stdout 2015-01-11T20:53:27.043967:   0    -0.702807   [ 0.999791 0.0359233 -0.00225278 -0.034834 0.991604 -0.131779 -0.00189553 0.134052 0.989003 5.06475 26.8036 6.42539 ]
INFO:interface:stdout 2015-01-11T20:53:27.216865:   1    -0.706264   [ 1.00134 0.0377896 -0.000865174 -0.0324745 0.99608 -0.126172 -0.000958112 0.13685 0.9815 5.13491 26.8114 6.40492 ]
INFO:interface:stdout 2015-01-11T20:53:27.385400:   2     -0.71206   [ 1.00124 0.0374643 -0.00102225 -0.0320857 0.996296 -0.126026 -0.000981607 0.136904 0.981777 4.97927 26.693 6.44184 ]
INFO:interface:stdout 2015-01-11T20:53:27.521869:   3    -0.714171   [ 1.00114 0.0373376 -0.000886938 -0.031404 0.996703 -0.124888 -0.000888575 0.136934 0.981713 5.00508 26.572 6.40613 ]
INFO:interface:stdout 2015-01-11T20:53:27.660222:   4    -0.715148   [ 1.00102 0.0371517 -0.00038632 -0.0301627 0.997732 -0.123255 -0.000574102 0.136942 0.981411 5.01982 26.571 6.37684 ]
INFO:interface:stdout 2015-01-11T20:53:27.827263:   5    -0.716083   [ 1.0009 0.0365815 0.000365988 -0.0289926 0.998843 -0.122051 -0.000215934 0.137071 0.982408 4.91811 26.3957 6.42315 ]
INFO:interface:stdout 2015-01-11T20:53:28.054741:   6    -0.716769   [ 1.00111 0.0366067 0.000530867 -0.0285424 0.999452 -0.12132 -5.44128e-05 0.137063 0.982578 5.01947 26.4856 6.37738 ]
INFO:interface:stdout 2015-01-11T20:53:28.196511:   7    -0.717475   [ 1.0013 0.0363345 0.00115994 -0.0275019 1.00074 -0.119861 0.00042117 0.137211 0.983282 5.034 26.5285 6.33642 ]
INFO:interface:stdout 2015-01-11T20:53:28.363052:   8    -0.718164   [ 1.00145 0.0360091 0.00130349 -0.0258933 1.00236 -0.11833 0.00103463 0.137694 0.984134 4.98105 26.4814 6.39034 ]
INFO:interface:stdout 2015-01-11T20:53:28.502717:   9    -0.718817   [ 1.00152 0.0361579 0.00116711 -0.0245352 1.00294 -0.117697 0.00164179 0.138203 0.984264 4.993 26.3892 6.34944 ]
INFO:interface:stdout 2015-01-11T20:53:28.790708:  10    -0.719448   [ 1.00152 0.0361773 0.00110743 -0.0242289 1.00308 -0.117516 0.00178872 0.138369 0.984262 4.99369 26.383 6.34053 ]
INFO:interface:stdout 2015-01-11T20:53:28.924109:  11    -0.719549   [ 1.00147 0.036157 0.000919475 -0.023851 1.00327 -0.117291 0.00194665 0.138634 0.98425 4.99591 26.3916 6.34781 ]
INFO:interface:stdout 2015-01-11T20:53:29.118678:  12    -0.719657   [ 1.00144 0.0361216 0.00081409 -0.0238306 1.00329 -0.117307 0.00193104 0.13864 0.984258 4.99574 26.3901 6.353 ]
INFO:interface:stdout 2015-01-11T20:53:29.284126:  13    -0.719674   [ 1.00142 0.0360896 0.000728222 -0.0238127 1.0033 -0.117304 0.00192065 0.138645 0.984245 4.99628 26.3896 6.35322 ]
INFO:interface:stdout 2015-01-11T20:53:29.421349:  14    -0.719716   [ 1.00132 0.0359724 0.00042293 -0.0237462 1.00335 -0.11728 0.0018845 0.138662 0.984192 4.99944 26.3882 6.35125 ]
INFO:interface:stdout 2015-01-11T20:53:29.565877:  15     -0.71978   [ 1.00088 0.0353833 -0.0010213 -0.0233972 1.00362 -0.117116 0.0017103 0.138739 0.984006 5.02117 26.376 6.33663 ]
INFO:interface:stdout 2015-01-11T20:53:29.847158:  16    -0.720019   [ 1.00072 0.035163 -0.00153329 -0.0232548 1.00372 -0.117045 0.00164312 0.138773 0.983954 5.03006 26.369 6.33123 ]
INFO:interface:stdout 2015-01-11T20:53:29.991372:  17    -0.720032   [ 1.00073 0.0351616 -0.00148728 -0.0232265 1.00373 -0.117029 0.0016377 0.138785 0.983971 5.03047 26.3654 6.33125 ]
INFO:interface:stdout 2015-01-11T20:53:30.125397:  18    -0.720081   [ 1.00075 0.0351582 -0.00141331 -0.0231797 1.00374 -0.117004 0.00162885 0.138807 0.984 5.03066 26.3604 6.33118 ]
INFO:interface:stdout 2015-01-11T20:53:30.290304:  19    -0.720108   [ 1.00078 0.0351508 -0.00131707 -0.0231168 1.00375 -0.116972 0.0016169 0.138837 0.984044 5.0306 26.356 6.33126 ]
INFO:interface:stdout 2015-01-11T20:53:30.433481:  20    -0.720134   [ 1.00082 0.0351331 -0.00117295 -0.0230173 1.00375 -0.116929 0.00159783 0.138884 0.98412 5.03104 26.3524 6.33266 ]
INFO:interface:stdout 2015-01-11T20:53:30.569889:  21    -0.720148   [ 1.00088 0.0350901 -0.000954414 -0.0228591 1.00374 -0.116873 0.00156936 0.138943 0.984269 5.03209 26.3492 6.33583 ]
INFO:interface:stdout 2015-01-11T20:53:30.732995:  22    -0.720175   [ 1.00091 0.0350142 -0.000724674 -0.0226799 1.00371 -0.116808 0.00154464 0.138983 0.98449 5.03401 26.3458 6.33851 ]
INFO:interface:stdout 2015-01-11T20:53:30.985826:  23      -0.7202   [ 1.00094 0.0349335 -0.000504897 -0.0224977 1.00367 -0.116735 0.00152005 0.139022 0.984684 5.03526 26.3435 6.33925 ]
INFO:interface:stdout 2015-01-11T20:53:31.241353:  24    -0.720225   [ 1.00096 0.0348718 -0.000343245 -0.0223601 1.00365 -0.116677 0.0015014 0.139051 0.98482 5.0359 26.342 6.3392 ]
INFO:interface:stdout 2015-01-11T20:53:31.432274:  25    -0.720228   [ 1.00096 0.0348612 -0.000318771 -0.0223368 1.00364 -0.116666 0.00149811 0.139055 0.984837 5.03582 26.3418 6.33886 ]
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INFO:interface:stdout 2015-01-11T20:53:31.912303:  28    -0.720237   [ 1.00096 0.0348562 -0.000321248 -0.0223273 1.00364 -0.116656 0.00149615 0.139055 0.984817 5.03502 26.342 6.33743 ]
INFO:interface:stdout 2015-01-11T20:53:32.056781:  29    -0.720239   [ 1.00096 0.0348536 -0.000322484 -0.0223222 1.00364 -0.116651 0.00149511 0.139054 0.984807 5.03463 26.342 6.33677 ]
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INFO:interface:stdout 2015-01-11T20:53:32.498237:  32    -0.720263   [ 1.00096 0.0348382 -0.000329042 -0.02229 1.00364 -0.116624 0.00148883 0.139052 0.984753 5.03265 26.3416 6.33389 ]
INFO:interface:stdout 2015-01-11T20:53:32.634354:  33     -0.72027   [ 1.00096 0.0348271 -0.000333173 -0.0222648 1.00363 -0.116607 0.00148394 0.139049 0.98472 5.03151 26.3409 6.33275 ]
INFO:interface:stdout 2015-01-11T20:53:32.776778:  34    -0.720292   [ 1.00096 0.0348099 -0.000338761 -0.0222217 1.00362 -0.116582 0.00147571 0.139043 0.984675 5.03012 26.3393 6.3322 ]
INFO:interface:stdout 2015-01-11T20:53:32.912606:  35    -0.720315   [ 1.00096 0.0347827 -0.000345639 -0.022144 1.00361 -0.116541 0.0014613 0.139031 0.984614 5.02872 26.3366 6.33319 ]
INFO:interface:stdout 2015-01-11T20:53:33.080393:  36     -0.72035   [ 1.00097 0.0347613 -0.000348759 -0.0220703 1.00359 -0.1165 0.00144849 0.139016 0.984571 5.02848 26.3349 6.33508 ]
INFO:interface:stdout 2015-01-11T20:53:33.217479:  37    -0.720383   [ 1.00098 0.0347304 -0.000353532 -0.0219501 1.00356 -0.116429 0.00142872 0.138989 0.984509 5.02818 26.3324 6.33718 ]
INFO:interface:stdout 2015-01-11T20:53:33.358533:  38    -0.720412   [ 1.00101 0.0346918 -0.000361854 -0.0217668 1.0035 -0.116322 0.0014007 0.138942 0.984453 5.02767 26.3283 6.33854 ]
INFO:interface:stdout 2015-01-11T20:53:33.521015:  39    -0.720455   [ 1.00106 0.0346352 -0.000369338 -0.0214684 1.00342 -0.116175 0.00135668 0.138869 0.984407 5.02613 26.3258 6.33869 ]
INFO:interface:stdout 2015-01-11T20:53:33.749482:  40    -0.720513   [ 1.00109 0.0346275 -0.000363776 -0.0213845 1.0034 -0.116158 0.00134512 0.138854 0.984432 5.02608 26.3262 6.33823 ]
INFO:interface:stdout 2015-01-11T20:53:34.396012:  41    -0.720516   [ 1.00109 0.0346275 -0.000363776 -0.0213845 1.0034 -0.116158 0.00134512 0.138854 0.984432 5.02608 26.3262 6.33823 ]
INFO:interface:stdout 2015-01-11T20:53:34.687922:  42    -0.720516   [ 1.00109 0.0346275 -0.000363776 -0.0213845 1.0034 -0.116158 0.00134512 0.138854 0.984432 5.02608 26.3262 6.33823 ]
INFO:interface:stdout 2015-01-11T20:53:34.916961:  43    -0.720516   [ 1.00109 0.0346275 -0.000363776 -0.0213845 1.0034 -0.116158 0.00134512 0.138854 0.984432 5.02608 26.3262 6.33823 ]
INFO:interface:stdout 2015-01-11T20:53:35.172088:  44    -0.720516   [ 1.00109 0.0346275 -0.000363776 -0.0213845 1.0034 -0.116158 0.00134512 0.138854 0.984432 5.02608 26.3262 6.33823 ]
INFO:interface:stdout 2015-01-11T20:53:35.369396:  45    -0.720516   [ 1.00109 0.0346275 -0.000363776 -0.0213845 1.0034 -0.116158 0.00134512 0.138854 0.984432 5.02608 26.3262 6.33823 ]
INFO:interface:stdout 2015-01-11T20:53:35.541350:  46    -0.720516   [ 1.00109 0.0346275 -0.000363776 -0.0213845 1.0034 -0.116158 0.00134512 0.138854 0.984432 5.02608 26.3262 6.33823 ]
INFO:interface:stdout 2015-01-11T20:53:35.715081:  47    -0.720516   [ 1.00109 0.0346275 -0.000363776 -0.0213845 1.0034 -0.116158 0.00134512 0.138854 0.984432 5.02608 26.3262 6.33823 ]
INFO:interface:stdout 2015-01-11T20:53:35.764569:Stop condition from optimizer.ConjugateGradientLineSearchOptimizerv4Template: Convergence checker passed at iteration 48.
INFO:workflow:Executing node GetRigidTransformInverse in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/GetRigidTransformInverse
INFO:workflow:Executing node MakeResamplerInFilesListNode in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/MakeResamplerInFilesListNode
INFO:workflow:Executing node ResampleToB0Space in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ResampleToB0Space
INFO:workflow:Executing node _ResampleToB0Space0 in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ResampleToB0Space/mapflow/_ResampleToB0Space0
INFO:workflow:Running:  BRAINSResample  --inputVolume /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ExtractBRAINFromHead/T2Stripped.nrrd --interpolationMode Linear --outputVolume T2toB0.nrrd --pixelType ushort --referenceVolume /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/EXTRACT_B0/B0_Image.nrrd --warpTransform /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/BFit_T2toB0/T2ToB0_RigidTransform.h5
INFO:interface:stdout 2015-01-11T20:53:36.149247:=====================================================
INFO:interface:stdout 2015-01-11T20:53:36.149247:Input Volume:     /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ExtractBRAINFromHead/T2Stripped.nrrd
INFO:interface:stdout 2015-01-11T20:53:36.149247:Reference Volume: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/EXTRACT_B0/B0_Image.nrrd
INFO:interface:stdout 2015-01-11T20:53:36.149247:Output Volume:    T2toB0.nrrd
INFO:interface:stdout 2015-01-11T20:53:36.149247:Pixel Type:       ushort
INFO:interface:stdout 2015-01-11T20:53:36.149247:Interpolation:    Linear
INFO:interface:stdout 2015-01-11T20:53:36.153163:Background Value: 0
INFO:interface:stdout 2015-01-11T20:53:36.153163:Warp By Transform: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/BFit_T2toB0/T2ToB0_RigidTransform.h5
INFO:interface:stdout 2015-01-11T20:53:36.153163:=====================================================
INFO:interface:stdout 2015-01-11T20:53:36.223863:Read ITK transform from file: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/BFit_T2toB0/T2ToB0_RigidTransform.h5
INFO:interface:stdout 2015-01-11T20:53:36.231379:HACK: 0  VersorRigid3DTransform
INFO:workflow:Executing node _ResampleToB0Space1 in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ResampleToB0Space/mapflow/_ResampleToB0Space1
INFO:workflow:Running:  BRAINSResample  --inputVolume /Shared/sinapse/CACHE/20141124_TrackOn_base_Results/HDNI_003/823955340/823955340_20080609_30/TissueClassify/complete_brainlabels_seg.nii.gz --interpolationMode Linear --outputVolume BRAINMaskToB0.nrrd --pixelType binary --referenceVolume /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/EXTRACT_B0/B0_Image.nrrd --warpTransform /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/BFit_T2toB0/T2ToB0_RigidTransform.h5
INFO:interface:stdout 2015-01-11T20:53:36.400364:=====================================================
INFO:interface:stdout 2015-01-11T20:53:36.400364:Input Volume:     /Shared/sinapse/CACHE/20141124_TrackOn_base_Results/HDNI_003/823955340/823955340_20080609_30/TissueClassify/complete_brainlabels_seg.nii.gz
INFO:interface:stdout 2015-01-11T20:53:36.400364:Reference Volume: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/EXTRACT_B0/B0_Image.nrrd
INFO:interface:stdout 2015-01-11T20:53:36.400364:Output Volume:    BRAINMaskToB0.nrrd
INFO:interface:stdout 2015-01-11T20:53:36.400364:Pixel Type:       binary
INFO:interface:stdout 2015-01-11T20:53:36.400364:Interpolation:    Linear
INFO:interface:stdout 2015-01-11T20:53:36.400364:Background Value: 0
INFO:interface:stdout 2015-01-11T20:53:36.400364:Warp By Transform: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/BFit_T2toB0/T2ToB0_RigidTransform.h5
INFO:interface:stdout 2015-01-11T20:53:36.400364:=====================================================
INFO:interface:stdout 2015-01-11T20:53:36.501606:Read ITK transform from file: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/BFit_T2toB0/T2ToB0_RigidTransform.h5
INFO:interface:stdout 2015-01-11T20:53:36.508270:HACK: 0  VersorRigid3DTransform
INFO:workflow:Executing node SaveDirectionCosineToMatrix in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/SaveDirectionCosineToMatrix
INFO:workflow:Executing node CreateAntsRegistrationMask in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/CreateAntsRegistrationMask
INFO:workflow:Executing node MakeForceDCFilesListNode in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/MakeForceDCFilesListNode
INFO:workflow:Executing node ForceDCtoID in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ForceDCtoID
INFO:workflow:Executing node _ForceDCtoID0 in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ForceDCtoID/mapflow/_ForceDCtoID0
INFO:workflow:Executing node _ForceDCtoID1 in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ForceDCtoID/mapflow/_ForceDCtoID1
INFO:workflow:Executing node _ForceDCtoID2 in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ForceDCtoID/mapflow/_ForceDCtoID2
INFO:workflow:Executing node antsReg_B0ToTransformedT2 in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/antsReg_B0ToTransformedT2
INFO:workflow:Running: antsRegistration --float 1 --restrict-deformation 0x1x0 --collapse-output-transforms 0 --dimensionality 3 --masks /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ForceDCtoID/mapflow/_ForceDCtoID2/IDDC_registrationMask.nrrd --initialize-transforms-per-stage 0 --interpolation Linear --output Tsyn --transform SyN[ 0.25, 3.0, 0.0 ] --metric MI[ /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ForceDCtoID/mapflow/_ForceDCtoID1/IDDC_T2toB0.nrrd, /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ForceDCtoID/mapflow/_ForceDCtoID0/IDDC_B0_Image.nrrd, 1, 32, None, 1 ] --convergence [ 70x50x40, 1e-06, 10 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 0 --use-histogram-matching 1 --winsorize-image-intensities [ 0.01, 0.99 ]  --write-composite-transform 1
INFO:interface:stdout 2015-01-11T20:53:37.790797:All_Command_lines_OK
INFO:interface:stdout 2015-01-11T20:53:37.790797:Using single precision for computations.
INFO:interface:stdout 2015-01-11T20:53:37.794590:  number of levels = 3
INFO:interface:stdout 2015-01-11T20:53:37.795145:  fixed image: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ForceDCtoID/mapflow/_ForceDCtoID1/IDDC_T2toB0.nrrd
INFO:interface:stdout 2015-01-11T20:53:37.795145:  moving image: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ForceDCtoID/mapflow/_ForceDCtoID0/IDDC_B0_Image.nrrd
INFO:interface:stdout 2015-01-11T20:53:37.805504:Dimension = 3
INFO:interface:stdout 2015-01-11T20:53:37.805504:Number of stages = 1
INFO:interface:stdout 2015-01-11T20:53:37.805504:Use Histogram Matching true
INFO:interface:stdout 2015-01-11T20:53:37.805504:Winsorize image intensities false
INFO:interface:stdout 2015-01-11T20:53:37.807123:Lower quantile = 0
INFO:interface:stdout 2015-01-11T20:53:37.807123:Upper quantile = 1
INFO:interface:stdout 2015-01-11T20:53:37.807123:Stage 1 State
INFO:interface:stdout 2015-01-11T20:53:37.807123:   Image metric = Mattes
INFO:interface:stdout 2015-01-11T20:53:37.807123:     Fixed image = Image (0x7fd823f23790)
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INFO:interface:stdout 2015-01-11T20:53:37.807123:  Reference Count: 2
INFO:interface:stdout 2015-01-11T20:53:37.807123:  Modified Time: 979
INFO:interface:stdout 2015-01-11T20:53:37.807123:  Debug: Off
INFO:interface:stdout 2015-01-11T20:53:37.807123:  Object Name: 
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INFO:interface:stdout 2015-01-11T20:53:37.807123:      Reference Count: 1
INFO:interface:stdout 2015-01-11T20:53:37.807123:      Modified Time: 793
INFO:interface:stdout 2015-01-11T20:53:37.807123:      Debug: Off
INFO:interface:stdout 2015-01-11T20:53:37.807123:      Object Name: 
INFO:interface:stdout 2015-01-11T20:53:37.807123:      Observers: 
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INFO:interface:stdout 2015-01-11T20:53:37.807123:
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INFO:interface:stdout 2015-01-11T20:53:37.807123:  Reference Count: 2
INFO:interface:stdout 2015-01-11T20:53:37.807123:  Modified Time: 980
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INFO:interface:stdout 2015-01-11T20:53:37.807123:      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, float>
INFO:interface:stdout 2015-01-11T20:53:37.807123:      Reference Count: 1
INFO:interface:stdout 2015-01-11T20:53:37.807123:      Modified Time: 974
INFO:interface:stdout 2015-01-11T20:53:37.807123:      Debug: Off
INFO:interface:stdout 2015-01-11T20:53:37.807123:      Object Name: 
INFO:interface:stdout 2015-01-11T20:53:37.807123:      Observers: 
INFO:interface:stdout 2015-01-11T20:53:37.807123:        none
INFO:interface:stdout 2015-01-11T20:53:37.807123:      Pointer: 0x106df1000
INFO:interface:stdout 2015-01-11T20:53:37.807123:      Container manages memory: true
INFO:interface:stdout 2015-01-11T20:53:37.807123:      Size: 802816
INFO:interface:stdout 2015-01-11T20:53:37.807123:      Capacity: 802816
INFO:interface:stdout 2015-01-11T20:53:37.807123:
INFO:interface:stdout 2015-01-11T20:53:37.807123:     Weighting = 1
INFO:interface:stdout 2015-01-11T20:53:37.807123:     Sampling strategy = none
INFO:interface:stdout 2015-01-11T20:53:37.807123:     Number of bins = 32
INFO:interface:stdout 2015-01-11T20:53:37.807123:     Radius = 4
INFO:interface:stdout 2015-01-11T20:53:37.807123:     Sampling percentage  = 1
INFO:interface:stdout 2015-01-11T20:53:37.807123:   Transform = SyN
INFO:interface:stdout 2015-01-11T20:53:37.807123:     Gradient step = 0.25
INFO:interface:stdout 2015-01-11T20:53:37.807123:     Update field sigma (voxel space) = 3
INFO:interface:stdout 2015-01-11T20:53:37.807123:     Total field sigma (voxel space) = 0
INFO:interface:stdout 2015-01-11T20:53:37.807123:     Update field time sigma = 0
INFO:interface:stdout 2015-01-11T20:53:37.807123:     Total field time sigma  = 0
INFO:interface:stdout 2015-01-11T20:53:37.807123:     Number of time indices = 0
INFO:interface:stdout 2015-01-11T20:53:37.807123:     Number of time point samples = 0
INFO:interface:stdout 2015-01-11T20:53:37.807123:Registration using 1 total stages.
INFO:interface:stdout 2015-01-11T20:53:37.807123:
INFO:interface:stdout 2015-01-11T20:53:37.807123:Stage 0
INFO:interface:stdout 2015-01-11T20:53:37.807123:  iterations = 70x50x40
INFO:interface:stdout 2015-01-11T20:53:37.807123:  convergence threshold = 1e-06
INFO:interface:stdout 2015-01-11T20:53:37.807123:  convergence window size = 10
INFO:interface:stdout 2015-01-11T20:53:37.807123:  number of levels = 3
INFO:interface:stdout 2015-01-11T20:53:37.807123:  Shrink factors (level 1 out of 3): [3, 3, 3]
INFO:interface:stdout 2015-01-11T20:53:37.807123:  Shrink factors (level 2 out of 3): [2, 2, 2]
INFO:interface:stdout 2015-01-11T20:53:37.807123:  Shrink factors (level 3 out of 3): [1, 1, 1]
INFO:interface:stdout 2015-01-11T20:53:37.807123:  smoothing sigmas per level: [2, 1, 0]
INFO:interface:stdout 2015-01-11T20:53:37.807123:  using the Mattes MI metric (number of bins = 32, weight = 1)
INFO:interface:stdout 2015-01-11T20:53:38.104661:  preprocessing:  histogram matching the images
INFO:interface:stdout 2015-01-11T20:53:38.105532:  Using default NONE metricSamplingStrategy 
INFO:interface:stdout 2015-01-11T20:53:38.152059:
INFO:interface:stdout 2015-01-11T20:53:38.152059:*** Running SyN registration (varianceForUpdateField = 3, varianceForTotalField = 0) ***
INFO:interface:stdout 2015-01-11T20:53:38.152059:
INFO:interface:stdout 2015-01-11T20:53:39.035329:XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
INFO:interface:stdout 2015-01-11T20:53:39.035329: 1DIAGNOSTIC,     1, -8.531786203384e-01, inf, 8.8335e-01, 8.8335e-01, 
INFO:interface:stdout 2015-01-11T20:53:39.292323: 1DIAGNOSTIC,     2, -9.865465164185e-01, inf, 1.1402e+00, 2.5685e-01, 
INFO:interface:stdout 2015-01-11T20:53:39.548565: 1DIAGNOSTIC,     3, -1.063436031342e+00, inf, 1.3965e+00, 2.5628e-01, 
INFO:interface:stdout 2015-01-11T20:53:39.798244: 1DIAGNOSTIC,     4, -1.104176521301e+00, inf, 1.6461e+00, 2.4963e-01, 
INFO:interface:stdout 2015-01-11T20:53:40.054453: 1DIAGNOSTIC,     5, -1.118425130844e+00, inf, 1.9022e+00, 2.5613e-01, 
INFO:interface:stdout 2015-01-11T20:53:40.310583: 1DIAGNOSTIC,     6, -1.114225387573e+00, inf, 2.1583e+00, 2.5610e-01, 
INFO:interface:stdout 2015-01-11T20:53:40.561142: 1DIAGNOSTIC,     7, -1.129664182663e+00, inf, 2.4088e+00, 2.5050e-01, 
INFO:interface:stdout 2015-01-11T20:53:40.806630: 1DIAGNOSTIC,     8, -1.116496920586e+00, inf, 2.6543e+00, 2.4543e-01, 
INFO:interface:stdout 2015-01-11T20:53:41.057769: 1DIAGNOSTIC,     9, -1.142594337463e+00, inf, 2.9053e+00, 2.5107e-01, 
INFO:interface:stdout 2015-01-11T20:53:41.302153: 1DIAGNOSTIC,    10, -1.118289470673e+00, 1.189781166613e-02, 3.1497e+00, 2.4433e-01, 
INFO:interface:stdout 2015-01-11T20:53:41.547091: 1DIAGNOSTIC,    11, -1.150226116180e+00, 5.739097949117e-03, 3.3945e+00, 2.4487e-01, 
INFO:interface:stdout 2015-01-11T20:53:41.793457: 1DIAGNOSTIC,    12, -1.121968030930e+00, 2.395603107288e-03, 3.6408e+00, 2.4627e-01, 
INFO:interface:stdout 2015-01-11T20:53:42.037738: 1DIAGNOSTIC,    13, -1.154148817062e+00, 1.551490277052e-03, 3.8850e+00, 2.4419e-01, 
INFO:interface:stdout 2015-01-11T20:53:42.282108: 1DIAGNOSTIC,    14, -1.125879287720e+00, 9.039489668794e-04, 4.1294e+00, 2.4439e-01, 
INFO:interface:stdout 2015-01-11T20:53:42.533438: 1DIAGNOSTIC,    15, -1.152964353561e+00, 9.940863819793e-04, 4.3807e+00, 2.5128e-01, 
INFO:interface:stdout 2015-01-11T20:53:42.785275: 1DIAGNOSTIC,    16, -1.137013435364e+00, 6.389441550709e-04, 4.6325e+00, 2.5177e-01, 
INFO:interface:stdout 2015-01-11T20:53:43.036188: 1DIAGNOSTIC,    17, -1.136991500854e+00, 5.151944933459e-04, 4.8833e+00, 2.5088e-01, 
INFO:interface:stdout 2015-01-11T20:53:43.286633: 1DIAGNOSTIC,    18, -1.135893344879e+00, 1.454243320040e-04, 5.1337e+00, 2.5038e-01, 
INFO:interface:stdout 2015-01-11T20:53:43.537082: 1DIAGNOSTIC,    19, -1.129161596298e+00, 7.311074296013e-05, 5.3841e+00, 2.5039e-01, 
INFO:interface:stdout 2015-01-11T20:53:43.791417: 1DIAGNOSTIC,    20, -1.135489344597e+00, -2.403228863841e-04, 5.6384e+00, 2.5428e-01, 
INFO:interface:stdout 2015-01-11T20:53:45.016928:XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
INFO:interface:stdout 2015-01-11T20:53:45.017798: 1DIAGNOSTIC,     1, -8.463570475578e-01, inf, 6.8639e+00, 1.2255e+00, 
INFO:interface:stdout 2015-01-11T20:53:45.784198: 1DIAGNOSTIC,     2, -8.816982507706e-01, inf, 7.6311e+00, 7.6717e-01, 
INFO:interface:stdout 2015-01-11T20:53:46.507058: 1DIAGNOSTIC,     3, -9.057378172874e-01, inf, 8.3539e+00, 7.2280e-01, 
INFO:interface:stdout 2015-01-11T20:53:47.250537: 1DIAGNOSTIC,     4, -9.157642126083e-01, inf, 9.0973e+00, 7.4343e-01, 
INFO:interface:stdout 2015-01-11T20:53:47.974820: 1DIAGNOSTIC,     5, -9.223705530167e-01, inf, 9.8215e+00, 7.2423e-01, 
INFO:interface:stdout 2015-01-11T20:53:48.718012: 1DIAGNOSTIC,     6, -9.280017018318e-01, inf, 1.0565e+01, 7.4314e-01, 
INFO:interface:stdout 2015-01-11T20:53:49.441780: 1DIAGNOSTIC,     7, -9.301456212997e-01, inf, 1.1288e+01, 7.2370e-01, 
INFO:interface:stdout 2015-01-11T20:53:50.188036: 1DIAGNOSTIC,     8, -9.346554279327e-01, inf, 1.2035e+01, 7.4620e-01, 
INFO:interface:stdout 2015-01-11T20:53:50.907728: 1DIAGNOSTIC,     9, -9.353750944138e-01, inf, 1.2754e+01, 7.1964e-01, 
INFO:interface:stdout 2015-01-11T20:53:51.651569: 1DIAGNOSTIC,    10, -9.403536319733e-01, 5.250083748251e-03, 1.3498e+01, 7.4379e-01, 
INFO:interface:stdout 2015-01-11T20:53:52.379869: 1DIAGNOSTIC,    11, -9.373646974564e-01, 2.983058569953e-03, 1.4226e+01, 7.2823e-01, 
INFO:interface:stdout 2015-01-11T20:53:53.146379: 1DIAGNOSTIC,    12, -9.454202651978e-01, 1.943490118720e-03, 1.4993e+01, 7.6643e-01, 
INFO:interface:stdout 2015-01-11T20:53:53.870939: 1DIAGNOSTIC,    13, -9.401756525040e-01, 1.330763916485e-03, 1.5717e+01, 7.2452e-01, 
INFO:interface:stdout 2015-01-11T20:53:54.635947: 1DIAGNOSTIC,    14, -9.456480741501e-01, 1.029021805152e-03, 1.6482e+01, 7.6496e-01, 
INFO:interface:stdout 2015-01-11T20:53:55.356082: 1DIAGNOSTIC,    15, -9.406942129135e-01, 7.042224751785e-04, 1.7202e+01, 7.2008e-01, 
INFO:interface:stdout 2015-01-11T20:53:56.117761: 1DIAGNOSTIC,    16, -9.473447203636e-01, 5.944634322077e-04, 1.7964e+01, 7.6161e-01, 
INFO:interface:stdout 2015-01-11T20:53:56.837417: 1DIAGNOSTIC,    17, -9.411232471466e-01, 3.643117088359e-04, 1.8683e+01, 7.1959e-01, 
INFO:interface:stdout 2015-01-11T20:53:57.576473: 1DIAGNOSTIC,    18, -9.493960142136e-01, 3.476763085928e-04, 1.9422e+01, 7.3900e-01, 
INFO:interface:stdout 2015-01-11T20:53:58.296247: 1DIAGNOSTIC,    19, -9.432647824287e-01, 2.086274471367e-04, 2.0142e+01, 7.1971e-01, 
INFO:interface:stdout 2015-01-11T20:53:59.081112: 1DIAGNOSTIC,    20, -9.496507644653e-01, 2.428919106023e-04, 2.0927e+01, 7.8481e-01, 
INFO:interface:stdout 2015-01-11T20:53:59.804185: 1DIAGNOSTIC,    21, -9.397912025452e-01, 5.851319656358e-05, 2.1650e+01, 7.2300e-01, 
INFO:interface:stdout 2015-01-11T20:54:00.546823: 1DIAGNOSTIC,    22, -9.507157206535e-01, 1.553654583404e-04, 2.2393e+01, 7.4258e-01, 
INFO:interface:stdout 2015-01-11T20:54:01.292576: 1DIAGNOSTIC,    23, -9.429265260696e-01, 4.918837294099e-05, 2.3138e+01, 7.4569e-01, 
INFO:interface:stdout 2015-01-11T20:54:02.035446: 1DIAGNOSTIC,    24, -9.511576294899e-01, 1.261512225028e-04, 2.3881e+01, 7.4283e-01, 
INFO:interface:stdout 2015-01-11T20:54:02.779360: 1DIAGNOSTIC,    25, -9.420899152756e-01, 1.008098570310e-05, 2.4625e+01, 7.4384e-01, 
INFO:interface:stdout 2015-01-11T20:54:03.518143: 1DIAGNOSTIC,    26, -9.507145881653e-01, 8.709025860298e-05, 2.5364e+01, 7.3871e-01, 
INFO:interface:stdout 2015-01-11T20:54:04.266103: 1DIAGNOSTIC,    27, -9.417924880981e-01, -2.680440775293e-05, 2.6111e+01, 7.4789e-01, 
INFO:interface:stdout 2015-01-11T20:54:10.950552:XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
INFO:interface:stdout 2015-01-11T20:54:10.951345: 1DIAGNOSTIC,     1, -5.817502737045e-01, inf, 3.2796e+01, 6.6845e+00, 
INFO:interface:stdout 2015-01-11T20:54:16.103850: 1DIAGNOSTIC,     2, -5.967645645142e-01, inf, 3.7949e+01, 5.1532e+00, 
INFO:interface:stdout 2015-01-11T20:54:21.252640: 1DIAGNOSTIC,     3, -6.093314886093e-01, inf, 4.3098e+01, 5.1487e+00, 
INFO:interface:stdout 2015-01-11T20:54:26.431391: 1DIAGNOSTIC,     4, -6.181748509407e-01, inf, 4.8277e+01, 5.1787e+00, 
INFO:interface:stdout 2015-01-11T20:54:31.751862: 1DIAGNOSTIC,     5, -6.249397993088e-01, inf, 5.3597e+01, 5.3204e+00, 
INFO:interface:stdout 2015-01-11T20:54:36.784765: 1DIAGNOSTIC,     6, -6.310904026031e-01, inf, 5.8630e+01, 5.0328e+00, 
INFO:interface:stdout 2015-01-11T20:54:41.792496: 1DIAGNOSTIC,     7, -6.360121369362e-01, inf, 6.3637e+01, 5.0077e+00, 
INFO:interface:stdout 2015-01-11T20:54:47.147064: 1DIAGNOSTIC,     8, -6.408026814461e-01, inf, 6.8992e+01, 5.3545e+00, 
INFO:interface:stdout 2015-01-11T20:54:52.125477: 1DIAGNOSTIC,     9, -6.454957723618e-01, inf, 7.3970e+01, 4.9784e+00, 
INFO:interface:stdout 2015-01-11T20:54:57.280233: 1DIAGNOSTIC,    10, -6.494910717010e-01, 6.463024765253e-03, 7.9125e+01, 5.1547e+00, 
INFO:interface:stdout 2015-01-11T20:55:02.411753: 1DIAGNOSTIC,    11, -6.524431705475e-01, 4.877131432295e-03, 8.4256e+01, 5.1314e+00, 
INFO:interface:stdout 2015-01-11T20:55:07.571062: 1DIAGNOSTIC,    12, -6.555419564247e-01, 3.802730469033e-03, 8.9416e+01, 5.1592e+00, 
INFO:interface:stdout 2015-01-11T20:55:12.739075: 1DIAGNOSTIC,    13, -6.575245261192e-01, 3.055559704080e-03, 9.4584e+01, 5.1680e+00, 
INFO:interface:stdout 2015-01-11T20:55:17.866779: 1DIAGNOSTIC,    14, -6.600020527840e-01, 2.501294948161e-03, 9.9711e+01, 5.1276e+00, 
INFO:interface:stdout 2015-01-11T20:55:22.998526: 1DIAGNOSTIC,    15, -6.617799997330e-01, 2.046959474683e-03, 1.0484e+02, 5.1317e+00, 
INFO:interface:stdout 2015-01-11T20:55:28.129515: 1DIAGNOSTIC,    16, -6.634685993195e-01, 1.680998364463e-03, 1.0997e+02, 5.1309e+00, 
INFO:interface:stdout 2015-01-11T20:55:33.292906: 1DIAGNOSTIC,    17, -6.646314859390e-01, 1.362808281556e-03, 1.1514e+02, 5.1633e+00, 
INFO:interface:stdout 2015-01-11T20:55:38.442692: 1DIAGNOSTIC,    18, -6.662508249283e-01, 1.111941179261e-03, 1.2029e+02, 5.1497e+00, 
INFO:interface:stdout 2015-01-11T20:55:43.608225: 1DIAGNOSTIC,    19, -6.672157049179e-01, 9.155716397800e-04, 1.2545e+02, 5.1655e+00, 
INFO:interface:stdout 2015-01-11T20:55:48.789792: 1DIAGNOSTIC,    20, -6.683213710785e-01, 7.663625874557e-04, 1.3063e+02, 5.1815e+00, 
INFO:interface:stdout 2015-01-11T20:55:53.962166: 1DIAGNOSTIC,    21, -6.694201231003e-01, 6.445613107644e-04, 1.3581e+02, 5.1723e+00, 
INFO:interface:stdout 2015-01-11T20:55:59.081875: 1DIAGNOSTIC,    22, -6.704967021942e-01, 5.571331712417e-04, 1.4093e+02, 5.1196e+00, 
INFO:interface:stdout 2015-01-11T20:56:04.290413: 1DIAGNOSTIC,    23, -6.714399456978e-01, 4.804072377738e-04, 1.4613e+02, 5.2085e+00, 
INFO:interface:stdout 2015-01-11T20:56:09.435026: 1DIAGNOSTIC,    24, -6.720611453056e-01, 4.214210202917e-04, 1.5128e+02, 5.1446e+00, 
INFO:interface:stdout 2015-01-11T20:56:14.615961: 1DIAGNOSTIC,    25, -6.729665398598e-01, 3.744589921553e-04, 1.5646e+02, 5.1809e+00, 
INFO:interface:stdout 2015-01-11T20:56:19.753278: 1DIAGNOSTIC,    26, -6.733393669128e-01, 3.303197445348e-04, 1.6160e+02, 5.1372e+00, 
INFO:interface:stdout 2015-01-11T20:56:24.919665: 1DIAGNOSTIC,    27, -6.740683317184e-01, 2.886064467020e-04, 1.6676e+02, 5.1663e+00, 
INFO:interface:stdout 2015-01-11T20:56:30.061799: 1DIAGNOSTIC,    28, -6.746039986610e-01, 2.560804423410e-04, 1.7191e+02, 5.1421e+00, 
INFO:interface:stdout 2015-01-11T20:56:35.217062: 1DIAGNOSTIC,    29, -6.753660440445e-01, 2.274059661431e-04, 1.7706e+02, 5.1552e+00, 
INFO:interface:stdout 2015-01-11T20:56:40.361058: 1DIAGNOSTIC,    30, -6.757825613022e-01, 2.009644376813e-04, 1.8220e+02, 5.1439e+00, 
INFO:interface:stdout 2015-01-11T20:56:45.511991: 1DIAGNOSTIC,    31, -6.765398979187e-01, 1.831115951063e-04, 1.8736e+02, 5.1509e+00, 
INFO:interface:stdout 2015-01-11T20:56:50.640044: 1DIAGNOSTIC,    32, -6.768341660500e-01, 1.673657825449e-04, 1.9248e+02, 5.1280e+00, 
INFO:interface:stdout 2015-01-11T20:56:55.823393: 1DIAGNOSTIC,    33, -6.773373484612e-01, 1.556739443913e-04, 1.9767e+02, 5.1833e+00, 
INFO:interface:stdout 2015-01-11T20:57:00.976378: 1DIAGNOSTIC,    34, -6.777344942093e-01, 1.426095986972e-04, 2.0282e+02, 5.1529e+00, 
INFO:interface:stdout 2015-01-11T20:57:06.123194: 1DIAGNOSTIC,    35, -6.781870126724e-01, 1.335116103292e-04, 2.0797e+02, 5.1468e+00, 
INFO:interface:stdout 2015-01-11T20:57:11.302866: 1DIAGNOSTIC,    36, -6.785477399826e-01, 1.208671237691e-04, 2.1315e+02, 5.1796e+00, 
INFO:interface:stdout 2015-01-11T20:57:16.449379: 1DIAGNOSTIC,    37, -6.791374683380e-01, 1.127634386648e-04, 2.1829e+02, 5.1465e+00, 
INFO:interface:stdout 2015-01-11T20:57:21.648182: 1DIAGNOSTIC,    38, -6.792256832123e-01, 1.012351276586e-04, 2.2349e+02, 5.1987e+00, 
INFO:interface:stdout 2015-01-11T20:57:26.819291: 1DIAGNOSTIC,    39, -6.799381971359e-01, 9.702470561024e-05, 2.2866e+02, 5.1710e+00, 
INFO:interface:stdout 2015-01-11T20:57:31.985947: 1DIAGNOSTIC,    40, -6.802145838737e-01, 9.093873813981e-05, 2.3383e+02, 5.1666e+00, 
INFO:interface:stdout 2015-01-11T20:57:32.228703:  Elapsed time (stage 0): 2.3442e+02
INFO:interface:stdout 2015-01-11T20:57:32.228703:
INFO:interface:stdout 2015-01-11T20:57:32.256260:
INFO:interface:stdout 2015-01-11T20:57:32.256260:Total elapsed time: 2.3445e+02
INFO:workflow:Executing node gtractResampleDWI_SyN in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/gtractResampleDWI_SyN
INFO:workflow:Running:  gtractResampleDWIInPlace  --inputVolume /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/DWI_ForceDCtoIDNode/IDDC_823955340_823955340_20080609_30_DWI_CONCAT_QCed_INSPECTED.nrrd --outputVolume IDDC_correctedDWI.nrrd --referenceVolume /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/ForceDCtoID/mapflow/_ForceDCtoID1/IDDC_T2toB0.nrrd --warpDWITransform /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/antsReg_B0ToTransformedT2/TsynComposite.h5
INFO:interface:stdout 2015-01-11T20:57:32.642664:=====================================================
INFO:interface:stdout 2015-01-11T20:57:32.642664:DWI Image: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/DWI_ForceDCtoIDNode/IDDC_823955340_823955340_20080609_30_DWI_CONCAT_QCed_INSPECTED.nrrd
INFO:interface:stdout 2015-01-11T20:57:32.642664:Input Transform: 
INFO:interface:stdout 2015-01-11T20:57:32.642664:warpDWI Transform: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/antsReg_B0ToTransformedT2/TsynComposite.h5
INFO:interface:stdout 2015-01-11T20:57:32.642664:Output Image: IDDC_correctedDWI.nrrd
INFO:interface:stdout 2015-01-11T20:57:32.642664:Debug Level: 0
INFO:interface:stdout 2015-01-11T20:57:32.642664:Image Output Size: 0,0,0
INFO:interface:stdout 2015-01-11T20:57:32.642664:=====================================================
INFO:interface:stdout 2015-01-11T20:57:32.738760:Read Image
INFO:interface:stdout 2015-01-11T20:57:32.739603:Read ITK transform from file: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/antsReg_B0ToTransformedT2/TsynComposite.h5
INFO:interface:stdout 2015-01-11T20:57:32.825137:HACK: 0  CompositeTransform
INFO:interface:stdout 2015-01-11T20:57:32.867959:Rigid transform matrix: 1 0 0
INFO:interface:stdout 2015-01-11T20:57:32.867959:0 1 0
INFO:interface:stdout 2015-01-11T20:57:32.867959:0 0 1
INFO:interface:stdout 2015-01-11T20:57:32.867959:
INFO:interface:stdout 2015-01-11T20:57:32.869753:Input DWI Image Origin: ( -109.009, -109.767, -56.6923 )
INFO:interface:stdout 2015-01-11T20:57:32.869753:Input DWI Image Size: 112 112 64
INFO:interface:stdout 2015-01-11T20:57:32.869753: 
INFO:interface:stdout 2015-01-11T20:57:32.869753:Output DWI Image Origin: ( -109.009, -109.767, -56.6923 )
INFO:interface:stdout 2015-01-11T20:57:32.869753:Output DWI Image Size: 112 112 64
INFO:workflow:Executing node RestoreDCFromSavedMatrix in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/RestoreDCFromSavedMatrix
INFO:workflow:Executing node gtractResampleDWIInPlace_Trigid in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/gtractResampleDWIInPlace_Trigid
INFO:workflow:Running:  gtractResampleDWIInPlace  --inputTransform /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/GetRigidTransformInverse/Inverse_T2ToB0_RigidTransform.h5 --inputVolume /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/RestoreDCFromSavedMatrix/correctedDWI.nrrd --outputResampledB0 CorrectedDWI_in_T2Space_B0.nrrd --outputVolume CorrectedDWI_in_T2Space.nrrd
INFO:interface:stdout 2015-01-11T20:57:36.888615:=====================================================
INFO:interface:stdout 2015-01-11T20:57:36.888615:DWI Image: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/RestoreDCFromSavedMatrix/correctedDWI.nrrd
INFO:interface:stdout 2015-01-11T20:57:36.888615:Input Transform: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/GetRigidTransformInverse/Inverse_T2ToB0_RigidTransform.h5
INFO:interface:stdout 2015-01-11T20:57:36.888615:warpDWI Transform: 
INFO:interface:stdout 2015-01-11T20:57:36.891329:Output Image: CorrectedDWI_in_T2Space.nrrd
INFO:interface:stdout 2015-01-11T20:57:36.891329:Debug Level: 0
INFO:interface:stdout 2015-01-11T20:57:36.891329:Image Output Size: 0,0,0
INFO:interface:stdout 2015-01-11T20:57:36.891329:=====================================================
INFO:interface:stdout 2015-01-11T20:57:36.986630:Read Image
INFO:interface:stdout 2015-01-11T20:57:36.987253:Read ITK transform from file: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/GetRigidTransformInverse/Inverse_T2ToB0_RigidTransform.h5
INFO:interface:stdout 2015-01-11T20:57:36.993286:HACK: 0  VersorRigid3DTransform
INFO:interface:stdout 2015-01-11T20:57:37.010255:Rigid transform matrix: 0.999615 -0.0277164 -0.00117917
INFO:interface:stdout 2015-01-11T20:57:37.010255:0.0276413 0.991493 0.127195
INFO:interface:stdout 2015-01-11T20:57:37.010255:-0.00235624 -0.127178 0.991877
INFO:interface:stdout 2015-01-11T20:57:37.010255:
INFO:interface:stdout 2015-01-11T20:57:37.011828:Input DWI Image Origin: ( -106.552, -72.1999, -62.3967 )
INFO:interface:stdout 2015-01-11T20:57:37.011828:Input DWI Image Size: 112 112 64
INFO:interface:stdout 2015-01-11T20:57:37.011828: 
INFO:interface:stdout 2015-01-11T20:57:37.011828:Output DWI Image Origin: ( -106.552, -72.1999, -62.3967 )
INFO:interface:stdout 2015-01-11T20:57:37.011828:Output DWI Image Size: 112 112 64
INFO:workflow:Executing node DWIBRAINMASK in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/DWIBRAINMASK
INFO:workflow:Running:  BRAINSResample  --inputVolume /Shared/sinapse/CACHE/20141124_TrackOn_base_Results/HDNI_003/823955340/823955340_20080609_30/TissueClassify/complete_brainlabels_seg.nii.gz --interpolationMode Linear --outputVolume BrainMaskForDWI.nrrd --pixelType binary --referenceVolume /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/gtractResampleDWIInPlace_Trigid/CorrectedDWI_in_T2Space_B0.nrrd
INFO:interface:stdout 2015-01-11T20:57:39.666314:=====================================================
INFO:interface:stdout 2015-01-11T20:57:39.666314:Input Volume:     /Shared/sinapse/CACHE/20141124_TrackOn_base_Results/HDNI_003/823955340/823955340_20080609_30/TissueClassify/complete_brainlabels_seg.nii.gz
INFO:interface:stdout 2015-01-11T20:57:39.668261:Reference Volume: /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/gtractResampleDWIInPlace_Trigid/CorrectedDWI_in_T2Space_B0.nrrd
INFO:interface:stdout 2015-01-11T20:57:39.668261:Output Volume:    BrainMaskForDWI.nrrd
INFO:interface:stdout 2015-01-11T20:57:39.668261:Pixel Type:       binary
INFO:interface:stdout 2015-01-11T20:57:39.668261:Interpolation:    Linear
INFO:interface:stdout 2015-01-11T20:57:39.668261:Background Value: 0
INFO:interface:stdout 2015-01-11T20:57:39.668261:Warp By Transform: Identity
INFO:interface:stdout 2015-01-11T20:57:39.668261:=====================================================
INFO:workflow:Executing node DTIEstim in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/DTIEstim
INFO:workflow:Running:  dtiestim  --brain_mask /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/DWIBRAINMASK/BrainMaskForDWI.nrrd --dwi_image /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/gtractResampleDWIInPlace_Trigid/CorrectedDWI_in_T2Space.nrrd --method wls --tensor_output DTI_Output.nrrd
INFO:interface:stdout 2015-01-11T20:57:40.922896:warning pixelsizes are off between mask and dwi, ignoring and masking nevertheless
INFO:workflow:Executing node DTIProcess in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/DTIProcess
INFO:workflow:Running:  dtiprocess  --RD_output RD.nrrd --dti_image /Volumes/scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/DTIEstim/DTI_Output.nrrd --fa_output FA.nrrd --frobenius_norm_output frobenius_norm_output.nrrd --lambda1_output lambda1_output.nrrd --lambda2_output lambda2_output.nrrd --lambda3_output lambda3_output.nrrd --md_output MD.nrrd --scalar_float 
INFO:workflow:Executing node DWIDataSink in dir: /scratch/TESTS/IpythonNotebook/1_DWI_Nipype_workflow/DWIWorkflow_823955340_20080609_30/DWIDataSink










    
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<networkx.classes.digraph.DiGraph at 0x11e2b4dd0>

















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Content source: aghayoor/SimpleITK-Notebook-Answers

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