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Last login: Mon Nov 7 14:48:24 on ttys000
Rons-MacBook-Pro:~ rkikinis$ cd Downloads/
Rons-MacBook-Pro:Downloads rkikinis$ ls
111108 Phantom fusion of EIT images with MRI - main ISMRM.pdf SceneviewTest
2011-09-02-Case40-EMBC Slicer-4.0.gamma-2011-11-03-macosx-amd64.app
2011-09-04-Neurodti Slicer-4.0.gamma-2011-11-04-macosx-amd64.app
2011-10-19-sceneviewtest Slicer-4.0.gamma-2011-11-07-macosx-amd64.app
2011-10-30-Door Slicer-4.0.gamma-2011-11-09-macosx-amd64.app
2011-11-08-Neurodti Slicer3-3.6.3-2011-03-04-stable-darwin-x86
Ankle Slicer3-3.6.3-2011-06-07-darwin-x86-London
AutomatedVertebralBodySegmentationPaper.docx Slicer3-3.6.4-beta-2011-11-06-darwin-x86
FemalePelvisAtlas2011v1 SoniaTestscene
HNMuscles-segmentation Suares
INTRuST_DUKE_V_003_20101129 VR-test-2011-09-16
Keep WindowsDownloads
MICCAI2011-Pat3 XNAT-Gateway-MacOS
NAC EngCore Year14 Budget.xls ZorasVCFS
NAC Year14 Budget.xls ctkDICOM-Database
SampleData mi2b2
Rons-MacBook-Pro:Downloads rkikinis$ cd Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/
Rons-MacBook-Pro:Slicer-4.0.gamma-2011-11-09-macosx-amd64.app rkikinis$ cd Contents/
Rons-MacBook-Pro:Contents rkikinis$ ls
Frameworks Info.plist MacOS Resources bin cli-modules lib share
Rons-MacBook-Pro:Contents rkikinis$ cd MacOS/
Rons-MacBook-Pro:MacOS rkikinis$ ls
Slicer
Rons-MacBook-Pro:MacOS rkikinis$ ./Slicer
3585 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - registerIO qSlicerFiducialsIO
Number of registered modules: 78
8893 [] DEBUG org.commontk.dicom.DICOMDatabase - Register compression libraries
starting DICOM listener
(u'Starting /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/bin/storescp with ', ['11112', '--output-directory', u'/Users/rkikinis/Downloads/ctkDICOM-Database/incoming', '--exec-on-reception', u'/Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/bin/dcmdump --load-short --print-short --print-filename --search PatientName /Users/rkikinis/Downloads/ctkDICOM-Database/incoming/#f'])
process /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/bin/storescp now in state Starting
2011-11-09 10:51:43.952 Slicer[14136:7303] invalid drawable
2011-11-09 10:51:43.953 Slicer[14136:7303] invalid drawable
Loading module "Cameras"
Loading module "EventBroker"
Loading module "VolumeRendering"
10686 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - registerIO qSlicerVolumeRenderingIO
Loading module "CropVolume"
Loading module "SceneViews"
Loading module "EMSegment"
Loading module "ViewControllers"
Loading module "Annotations"
Loading module "Models"
10703 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - registerIO qSlicerModelsIO
10703 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - registerIO qSlicerScalarOverlayIO
Loading module "ModuleTemplate"
Loading module "Transforms"
10709 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - registerIO qSlicerTransformsIO
Loading module "TractographyFiducialSeeding"
Loading module "Tractography"
Loading module "Data"
10712 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - registerIO qSlicerSceneIO
10712 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - registerIO qSlicerSlicer2SceneReader
10712 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - registerIO qSlicerXcedeCatalogIO
Loading module "EMSegmentQuick"
Loading module "Welcome"
Loading module "Colors"
10723 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - registerIO qSlicerColorsIO
QSortFilterProxyModel: index from wrong model passed to mapToSource
Loading module "TractographyDisplay"
11135 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - registerIO qSlicerFiberBundleIO
Loading module "Volumes"
11136 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - registerIO qSlicerVolumesIO
Loading module "LabelStatistics"
Loading module "PerformanceTests"
Loading module "Endoscopy"
Loading module "SampleData"
Loading module "DICOM2FullBrainTractography"
Loading module "DataProbe"
Loading module "DICOM"
Loading module "ChangeTracker"
Loading module "Editor"
Loading module "BRAINSResample"
Loading module "Mask"
Loading module "dwiNoiseFilter"
Loading module "CurvatureAnisotropicDiffusion"
Loading module "MedianImageFilter"
Loading module "ExtractSkeleton"
Loading module "CheckerBoard"
Loading module "MultipleModelsExample"
Loading module "ResampleDTI"
Loading module "GrayscaleFillHoleImageFilter"
Loading module "ConfidenceConnected"
Loading module "HistogramMatching"
Loading module "dwiUNLM"
Loading module "BRAINSFit"
Loading module "SparseFieldLevelSetContour"
Loading module "ComputeSUVBodyWeight"
Loading module "RobustStatSegmenter"
Loading module "MergeModels"
Loading module "ModelMaker"
Loading module "DicomToNrrdConverter"
Loading module "jointLMMSE"
Loading module "VotingBinaryHoleFillingImageFilter"
Loading module "Realign"
Loading module "Threshold"
Loading module "OrientImage"
Loading module "Add"
Loading module "N4ITKBiasFieldCorrection"
Loading module "Multiply"
Loading module "LabelMapSmoothing"
Loading module "ResampleVolume2"
Loading module "GradientAnisotropicDiffusion"
Loading module "Subtract"
Loading module "ImageLabelCombine"
Loading module "Cast"
Loading module "ExecutionModelTour"
Loading module "GaussianBlurImageFilter"
Loading module "GrayscaleGrindPeakImageFilter"
Loading module "BRAINSROIAuto"
Loading module "PolyDataToLabelmap"
Loading module "ImageReadDicomWrite"
Loading module "DiffusionWeightedMasking"
Loading module "EMSegmentTransformToNewFormat"
Loading module "DemonsSegmentationMetric"
Loading module "IntensityDifferenceMetric"
Loading module "Seeding"
Loading module "EMSegmentCommandLine"
Loading module "DiffusionTensorMathematics"
Loading module "ProbeVolumeWithModel"
Loading module "DiffusionTensorEstimation"
Loading module "GrayscaleModelMaker"
Number of loaded modules: 78
Show module (name): "Welcome"
process /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/bin/storescp now in state Running
process /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/bin/storescp now in state NotRunning
error code is: 5
standard out is:
standard error is: E: cannot create network: 0006:031c TCP Initialization Error: Address already in use
"Volume" Reader has successfully read the file "/Users/rkikinis/Downloads/SampleData/MR-head.nrrd"
Show module (name): "EMSegment"
51839 [] DEBUG org.commontk.libs.core.ctkWorkflow - onEntryInternal - entering input from 1. Define Task
51839 [] DEBUG org.commontk.libs.core.ctkWorkflow - processingAfterOnEntry
51840 [] DEBUG org.commontk.libs.widgets.ctkWorkflowWidgetStep - showUserInterface - showing 1. Define Task
GetTclTaskDirectory::Copying task files ...
from: /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
to: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy
[EMSegmentPy 11/09/2011 10:52:25]: Added to List Task: 'CT Hand Bone' File : '/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/CT-Hand-Bone.mrml'
[EMSegmentPy 11/09/2011 10:52:25]: Added to List Task: 'Human Eye' File : '/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/Human-Eye.mrml'
[EMSegmentPy 11/09/2011 10:52:25]: Added to List Task: 'Lesion Exp' File : '/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/Lesion-Exp.mrml'
[EMSegmentPy 11/09/2011 10:52:25]: Added to List Task: 'MRI Human Brain Exp' File : '/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Exp.mrml'
[EMSegmentPy 11/09/2011 10:52:25]: Added to List Task: 'MRI Human Brain Full Parcellation' File : '/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Full-Parcellation.mrml'
[EMSegmentPy 11/09/2011 10:52:25]: Added to List Task: 'MRI Human Brain Hemisphere' File : '/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Hemisphere.mrml'
[EMSegmentPy 11/09/2011 10:52:25]: Added to List Task: 'MRI Human Brain HIPR' File : '/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-HIPR.mrml'
[EMSegmentPy 11/09/2011 10:52:25]: Added to List Task: 'MRI Human Brain Parcellation' File : '/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Parcellation.mrml'
[EMSegmentPy 11/09/2011 10:52:25]: Added to List Task: 'MRI Human Brain' File : '/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.mrml'
[EMSegmentPy 11/09/2011 10:52:25]: Added to List Task: 'Non Human Primate' File : '/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/Non-Human-Primate.mrml'
[EMSegmentPy 11/09/2011 10:52:25]: Added to List Task: 'Test Atlas Cluster' File : '/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/Test-Atlas-Cluster.mrml'
GetTclTaskDirectory::Copying task files ...
from: /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
to: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy
55064 [] INFO org.commontk.libs.core.ctkWorkflow - goForward - posting ValidationTransition
55067 [] INFO org.commontk.libs.core.ctkWorkflow - attemptToGoToNextStep - Attempting to go to the next step
55067 [] DEBUG org.commontk.libs.core.ctkWorkflow - validateInternal - validating input from 1. Define Task
[EMSegmentPy 11/09/2011 10:52:28]: Attempting to load task 'MRI Human Brain' from file '/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.mrml'
== Completed importing data /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.mrml
BiasCorrectionType: 0
UseLLS_Recompute_Means: 0
BiasCorrectionType: 0
UseLLS_Recompute_Means: 0
BiasCorrectionType: 0
UseLLS_Recompute_Means: 0
[EMSegmentPy 11/09/2011 10:52:30]: Loading completed.
GetTclTaskDirectory::Copying task files ...
from: /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
to: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy
56583 [] DEBUG org.commontk.libs.core.ctkWorkflow - goToNextStepAfterSuccessfulValidation - Calidation succeeded
56583 [] INFO org.commontk.libs.core.ctkWorkflow - goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
56583 [] DEBUG org.commontk.libs.core.ctkWorkflow - performTransitionBetweenSteps - Performing transition between steps
56584 [] DEBUG org.commontk.libs.core.ctkWorkflow - onExitInternal - exiting 1. Define Task
56584 [] DEBUG org.commontk.libs.core.ctkWorkflow - onEntryInternal - entering input from 2. Define Input Datasets
56584 [] DEBUG org.commontk.libs.core.ctkWorkflow - processingAfterOnEntry
56586 [] DEBUG org.commontk.libs.widgets.ctkWorkflowGroupBox - updateClientArea - hiding 1. Define Task
56589 [] DEBUG org.commontk.libs.widgets.ctkWorkflowWidgetStep - showUserInterface - showing 2. Define Input Datasets
GetTclTaskDirectory::Copying task files ...
from: /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
to: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy
GetTclTaskDirectory::Copying task files ...
from: /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
to: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy
Sourcing general Task file : /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/GenericTask.tcl
Sourcing task specific file: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
64016 [] INFO org.commontk.libs.core.ctkWorkflow - goToStep - Attempting to go to finish step Segment
64016 [] INFO org.commontk.libs.core.ctkWorkflow - goForward - posting ValidationTransition
64018 [] INFO org.commontk.libs.core.ctkWorkflow - attemptToGoToNextStep - Attempting to go to the next step
64019 [] DEBUG org.commontk.libs.core.ctkWorkflow - validateInternal - validating input from 2. Define Input Datasets
64019 [] DEBUG org.commontk.libs.core.ctkWorkflow - goToNextStepAfterSuccessfulValidation - Calidation succeeded
64019 [] INFO org.commontk.libs.core.ctkWorkflow - goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
64019 [] DEBUG org.commontk.libs.core.ctkWorkflow - performTransitionBetweenSteps - Performing transition between steps
64019 [] DEBUG org.commontk.libs.core.ctkWorkflow - onExitInternal - exiting 2. Define Input Datasets
64020 [] DEBUG org.commontk.libs.core.ctkWorkflow - onEntryInternal - entering input from 3. Define Anatomical Tree
64020 [] DEBUG org.commontk.libs.core.ctkWorkflow - processingAfterOnEntry
64020 [] INFO org.commontk.libs.core.ctkWorkflow - goForward - posting ValidationTransition
64020 [] INFO org.commontk.libs.core.ctkWorkflow - attemptToGoToNextStep - Attempting to go to the next step
64020 [] DEBUG org.commontk.libs.core.ctkWorkflow - validateInternal - validating input from 3. Define Anatomical Tree
64020 [] DEBUG org.commontk.libs.core.ctkWorkflow - goToNextStepAfterSuccessfulValidation - Calidation succeeded
64020 [] INFO org.commontk.libs.core.ctkWorkflow - goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
64020 [] DEBUG org.commontk.libs.core.ctkWorkflow - performTransitionBetweenSteps - Performing transition between steps
64020 [] DEBUG org.commontk.libs.core.ctkWorkflow - onExitInternal - exiting 3. Define Anatomical Tree
64020 [] DEBUG org.commontk.libs.core.ctkWorkflow - onEntryInternal - entering input from 4. Define Atlas
64020 [] DEBUG org.commontk.libs.core.ctkWorkflow - processingAfterOnEntry
64020 [] INFO org.commontk.libs.core.ctkWorkflow - goForward - posting ValidationTransition
64020 [] INFO org.commontk.libs.core.ctkWorkflow - attemptToGoToNextStep - Attempting to go to the next step
64021 [] DEBUG org.commontk.libs.core.ctkWorkflow - validateInternal - validating input from 4. Define Atlas
64021 [] DEBUG org.commontk.libs.core.ctkWorkflow - goToNextStepAfterSuccessfulValidation - Calidation succeeded
64021 [] INFO org.commontk.libs.core.ctkWorkflow - goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
64021 [] DEBUG org.commontk.libs.core.ctkWorkflow - performTransitionBetweenSteps - Performing transition between steps
64021 [] DEBUG org.commontk.libs.core.ctkWorkflow - onExitInternal - exiting 4. Define Atlas
64021 [] DEBUG org.commontk.libs.core.ctkWorkflow - onEntryInternal - entering input from 5. Edit Registration Parameters
64021 [] DEBUG org.commontk.libs.core.ctkWorkflow - processingAfterOnEntry
64021 [] INFO org.commontk.libs.core.ctkWorkflow - goForward - posting ValidationTransition
64021 [] INFO org.commontk.libs.core.ctkWorkflow - attemptToGoToNextStep - Attempting to go to the next step
64021 [] DEBUG org.commontk.libs.core.ctkWorkflow - validateInternal - validating input from 5. Edit Registration Parameters
64021 [] DEBUG org.commontk.libs.core.ctkWorkflow - goToNextStepAfterSuccessfulValidation - Calidation succeeded
64021 [] INFO org.commontk.libs.core.ctkWorkflow - goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
64021 [] DEBUG org.commontk.libs.core.ctkWorkflow - performTransitionBetweenSteps - Performing transition between steps
64021 [] DEBUG org.commontk.libs.core.ctkWorkflow - onExitInternal - exiting 5. Edit Registration Parameters
64021 [] DEBUG org.commontk.libs.core.ctkWorkflow - onEntryInternal - entering input from 6. Define Preprocessing
64021 [] DEBUG org.commontk.libs.core.ctkWorkflow - processingAfterOnEntry
64021 [] INFO org.commontk.libs.core.ctkWorkflow - goForward - posting ValidationTransition
GetTclTaskDirectory::Copying task files ...
from: /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
to: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy
GetTclTaskDirectory::Copying task files ...
from: /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
to: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy
Sourcing general Task file : /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/GenericTask.tcl
Sourcing task specific file: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
GetTclTaskDirectory::Copying task files ...
from: /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
to: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy
GetTclTaskDirectory::Copying task files ...
from: /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
to: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy
Sourcing general Task file : /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/GenericTask.tcl
Sourcing task specific file: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
TCL: ==========================================
TCL: == Init Variables
TCL: ==========================================
TCL: User selected BRAINS
TCLMRI: Preprocessing MRI Human Brain - ShowUserInterface
64381 [] INFO org.commontk.libs.core.ctkWorkflow - attemptToGoToNextStep - Attempting to go to the next step
64381 [] DEBUG org.commontk.libs.core.ctkWorkflow - validateInternal - validating input from 6. Define Preprocessing
64381 [] DEBUG org.commontk.libs.core.ctkWorkflow - goToNextStepAfterSuccessfulValidation - Calidation succeeded
64381 [] INFO org.commontk.libs.core.ctkWorkflow - goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
64382 [] DEBUG org.commontk.libs.core.ctkWorkflow - performTransitionBetweenSteps - Performing transition between steps
64382 [] DEBUG org.commontk.libs.core.ctkWorkflow - onExitInternal - exiting 6. Define Preprocessing
TCLMRI: ==========================================
TCLMRI: == Preprocress Data
TCLMRI: ==========================================
TCL: GetEntryValueFromMRML: :C1:C1
TCL: GetEntryValueFromMRML: {C1} {C1}
TCL: GetEntryValueFromMRML: :C1:C1
TCL: GetEntryValueFromMRML: {C1} {C1}
TCL: ==========================================
TCL: == InitPreprocessing
TCL: ==========================================
TCL: ==========================================
TCL: == Remove Negative Values
TCL: ==========================================
TCL: Start thresholding target image - start
TCL: Start thresholding target image - stop
TCL: 1 targetNodes detected
TCL: ==========================================
TCL: == Register Input Images --
TCL: ==========================================
TCL: ===> Skipping Registration of Target To Target
TCLMRI: ==> Preprocessing Setting: 1 1
TCL: ==========================================
TCL: == Intensity Correction
TCL: ==========================================
TCL: ==========================================
TCL: == N4ITKBiasFieldCorrectionCLI ==
TCL: ==========================================
TCL: Create file: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn936132899Pw68eu_vtkMRMLScalarVolumeNode9.nrrd
TCL: Create file: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn1120435571H44lbc_vtkMRMLScalarVolumeNode10.nrrd
/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn1120435571H44lbc_vtkMRMLScalarVolumeNode10.nrrd
TCL: Executing /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/cli-modules//N4ITKBiasFieldCorrection --inputimage "/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn936132899Pw68eu_vtkMRMLScalarVolumeNode9.nrrd" --outputimage "/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn1120435571H44lbc_vtkMRMLScalarVolumeNode10.nrrd"
TCL: Mask no read. Creaing Otsu mask.
<filter-start>
<filter-name>N4MRIBiasFieldCorrectionImageFilter</filter-name>
<filter-comment> "N4 Bias field correction" </filter-comment>
</filter-start>
<filter-progress>0</filter-progress>
Progress: 0
<filter-progress>0.00833333</filter-progress>
Progress: 0.00833333
<filter-progress>0.0166667</filter-progress>
Progress: 0.0166667
<filter-progress>0.025</filter-progress>
Progress: 0.025
<filter-progress>0.0333333</filter-progress>
Progress: 0.0333333
<filter-progress>0.0416667</filter-progress>
Progress: 0.0416667
<filter-progress>0.05</filter-progress>
Progress: 0.05
<filter-progress>0.0583333</filter-progress>
Progress: 0.0583333
<filter-progress>0.0666667</filter-progress>
Progress: 0.0666667
<filter-progress>0.075</filter-progress>
Progress: 0.075
<filter-progress>0.0833333</filter-progress>
Progress: 0.0833333
<filter-progress>0.0916667</filter-progress>
Progress: 0.0916667
<filter-progress>0.1</filter-progress>
Progress: 0.1
<filter-progress>0.108333</filter-progress>
Progress: 0.108333
<filter-progress>0.116667</filter-progress>
Progress: 0.116667
<filter-progress>0.125</filter-progress>
Progress: 0.125
<filter-progress>0.133333</filter-progress>
Progress: 0.133333
<filter-progress>0.141667</filter-progress>
Progress: 0.141667
<filter-progress>0.15</filter-progress>
Progress: 0.15
<filter-progress>0.158333</filter-progress>
Progress: 0.158333
<filter-progress>0.166667</filter-progress>
Progress: 0.166667
<filter-progress>0.175</filter-progress>
Progress: 0.175
<filter-progress>0.183333</filter-progress>
Progress: 0.183333
<filter-progress>0.191667</filter-progress>
Progress: 0.191667
<filter-progress>0.2</filter-progress>
Progress: 0.2
<filter-progress>0.208333</filter-progress>
Progress: 0.208333
<filter-progress>0.216667</filter-progress>
Progress: 0.216667
<filter-progress>0.225</filter-progress>
Progress: 0.225
<filter-progress>0.233333</filter-progress>
Progress: 0.233333
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<filter-name>N4MRIBiasFieldCorrectionImageFilter</filter-name>
<filter-time>150.502</filter-time>
</filter-end> N4MRIBiasFieldCorrectionImageFilter (0x1023b31c0)
RTTI typeinfo: itk::N4MRIBiasFieldCorrectionImageFilter<itk::Image<float, 3u>, itk::Image<unsigned char, 3u>, itk::Image<float, 3u> >
Reference Count: 1
Modified Time: 360
Debug: Off
Observers:
IterationEvent(Command)
Number Of Required Inputs: 1
Number Of Required Outputs: 1
Number Of Threads: 8
ReleaseDataFlag: Off
ReleaseDataBeforeUpdateFlag: Off
Input 0: (0x10c4002e0)
Input 1: (0x10c400740)
Output 0: (0x1023efd00)
AbortGenerateData: Off
Progress: 1
Multithreader:
RTTI typeinfo: itk::MultiThreader
Reference Count: 1
Modified Time: 7
Debug: Off
Observers:
none
Thread Count: 8
Global Maximum Number Of Threads: 128
Global Default Number Of Threads: 8
Mask label:
Number of histogram bins: 200
Wiener filter noise: 0.01
Bias field FWHM: 0.15
Maximum number of iterations: [50, 40, 30]
Convergence threshold: 0.0001
Spline order: 3
Number of fitting levels: [3, 3, 3]
Number of control points: [4, 4, 4]
CurrentConvergenceMeasurement: 0.000933366
CurrentLevel: 3
ElapsedIterations: 31
LogBiasFieldControlPointLattice: Image (0x10c401ba0)
RTTI typeinfo: itk::Image<itk::Vector<float, 1u>, 3u>
Reference Count: 2
Modified Time: 67389564
Debug: Off
Observers:
none
Source: (none)
Source output index: 0
Release Data: Off
Data Released: False
Global Release Data: Off
PipelineMTime: 0
UpdateMTime: 0
LargestPossibleRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [7, 7, 7]
BufferedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [7, 7, 7]
RequestedRegion:
Dimension: 3
Index: [0, 0, 0]
Size: [7, 7, 7]
Spacing: [1, 1, 1]
Origin: [0, 0, 0]
Direction:
1 0 0
0 1 0
0 0 1
IndexToPointMatrix:
1 0 0
0 1 0
0 0 1
PointToIndexMatrix:
1 0 0
0 1 0
0 0 1
PixelContainer:
ImportImageContainer (0x10c401e10)
RTTI typeinfo: itk::ImportImageContainer<unsigned long, itk::Vector<float, 1u> >
Reference Count: 1
Modified Time: 67389565
Debug: Off
Observers:
none
Pointer: 0x10c801000
Container manages memory: true
Size: 343
Capacity: 343
Elapsed ime: 150.502
TCL: ReadDataFromDisk: Try to read /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn1120435571H44lbc_vtkMRMLScalarVolumeNode10.nrrd
TCL: List of volume nodes: vtkMRMLScalarVolumeNode0x134f21998
TCL: 1 targetNodes detected
TCL: ==========================================
TCL: == Register Atlas
TCL: ==========================================
TCL: == (1 / 1)
TCL: ==========================================
TCL: Aligned Atlas was empty
TCL: Aligned SubParcellation was empty
TCL: ========== Info =========
TCL: = Fixed: MR-head1_pos(Aligned)1_N4corrected
TCL: = Moving: atlas_t1
TCL: = Affine: 2
TCL: = BSpline: 2
TCL: = Interp: 0
TCL: =========================
Background level guess :
first place: 0 (45.5455%)
second place: 2 (11.4007%)
Guessed background level: 0
TCL: ==========================================
TCL: == BRAINSRegistration: affine: 2 , deformable: 2
TCL: ==========================================
TCL: Create file: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn2024024901LHrAPx_vtkMRMLScalarVolumeNode10.nrrd
TCL: Create file: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn1645542627uBTE3Q_vtkMRMLScalarVolumeNode7.nrrd
TCL: Create file: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn13405259232cIAeZ_vtkMRMLScalarVolumeNode16.nrrd
TCL: Create file: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn968247184XIDPJB_vtkMRMLBSplineTransformNode1.mat
TCL: Executing "/Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/cli-modules//BRAINSFit" --backgroundFillValue 0.0 --interpolationMode Linear --outputVolumePixelType short --fixedVolume "/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn2024024901LHrAPx_vtkMRMLScalarVolumeNode10.nrrd" --movingVolume "/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn1645542627uBTE3Q_vtkMRMLScalarVolumeNode7.nrrd" --outputVolume "/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn13405259232cIAeZ_vtkMRMLScalarVolumeNode16.nrrd" --bsplineTransform "/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn968247184XIDPJB_vtkMRMLBSplineTransformNode1.mat" --numberOfIterations 1500 --numberOfSamples 300000 --useRigid --useScaleSkewVersor3D --useAffine --useBSpline --splineGridSize 6,6,6 --maxBSplineDisplacement 0 --useCachingOfBSplineWeightsMode ON --initializeTransformMode useCenterOfHeadAlign --minimumStepLength 0.005 --translationScale 1000 --reproportionScale 1 --skewScale 1 --maskProcessingMode NOMASK --numberOfHistogramBins 40 --numberOfMatchPoints 10 --costMetric MMI --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --debugNumberOfThreads -1 --debugLevel 0 --failureExitCode -1
TCL: Long flag "--debugNumberOfThreads" is deprecated. Please use long flag "--numberOfThreads" instead.
Original Fixed image origin[86.6449, -133.929, 116.786, 0]
TranformTypes: Rigid(1 of 4).
TranformTypes: ScaleSkewVersor3D(2 of 4).
TranformTypes: Affine(3 of 4).
TranformTypes: BSpline(4 of 4).
Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is 8126464
362 ValidHistogramsEntries, 8126464 TotalFrequency
0.001 ---> 0
0.999 ---> 219
LowHigh Thresholds: [44,-2147483648]
maxSIDirection = 119.531
Computing Sampled Distance Computations
ListSample TotalFrequency is 8519680
232 ValidHistogramsEntries, 8519680 TotalFrequency
0.001 ---> 0
0.999 ---> 137
LowHigh Thresholds: [38,-2147483648]
maxSIDirection = 116.786
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to
VersorRigid3DTransform (0x102bc84d0)
RTTI typeinfo: itk::VersorRigid3DTransform<double>
Reference Count: 2
Modified Time: 5191
Debug: Off
Observers:
none
Matrix:
0.994522 -0.104385 -0.0054706
0.104528 0.993159 0.0520493
4.33681e-19 -0.052336 0.99863
Offset: [0.243121, -6.15496, 3.5364]
Center: [0.407722, 1.72269, -7.67635]
Translation: [0.103058, -6.52367, 3.45676]
Inverse:
0.994522 0.104528 4.33681e-19
-0.104385 0.993159 -0.052336
-0.0054706 0.0520493 0.99863
Singular: 0
Versor: [ -0.0261411, -0.00137, 0.052318, 0.998287 ]
===============================================
=============================== Starting Transform Estimations for Rigid(1 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001].
0 -0.325435 [-0.0257509, 0.00134828, 0.050367, -0.0190123, -6.67608, 3.49948]
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2 -0.326582 [-0.0187538, 0.0206509, 0.042598, -0.066248, -7.04409, 3.48602]
3 -0.327757 [-0.0122603, 0.0306886, 0.0386177, -0.180837, -7.20177, 3.449]
4 -0.327329 [-0.00540669, 0.0254566, 0.0378497, -0.206431, -7.39423, 3.49378]
5 -0.326982 [0.00131571, 0.023211, 0.0491853, -0.212268, -7.58526, 3.44124]
6 -0.327938 [7.75413e-05, 0.0278064, 0.0463178, -0.320338, -7.73973, 3.3754]
7 -0.327881 [-0.00195929, 0.0234677, 0.0505129, -0.328977, -7.93347, 3.42259]
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10 -0.325822 [0.0170477, 0.0277992, 0.040568, -0.646513, -8.17043, 3.07715]
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12 -0.327226 [0.0117662, 0.0290914, 0.0399938, -0.58155, -8.34343, 2.72844]
13 -0.328777 [0.0132388, 0.0285239, 0.0432527, -0.512038, -8.52174, 2.67083]
14 -0.329084 [0.0125859, 0.022662, 0.0365907, -0.562151, -8.62979, 2.51115]
15 -0.330067 [0.0261673, 0.039622, 0.0365977, -0.482866, -8.69872, 2.34661]
16 -0.324985 [0.0273025, 0.0293788, 0.0360655, -0.325942, -8.62522, 2.24891]
17 -0.32638 [0.0222829, 0.0285578, 0.0342156, -0.398562, -8.56475, 2.27978]
18 -0.327718 [0.020386, 0.0270361, 0.036554, -0.362739, -8.5367, 2.29939]
19 -0.328598 [0.0174966, 0.0253802, 0.0350908, -0.385393, -8.49276, 2.29765]
20 -0.329459 [0.014832, 0.0271718, 0.0353278, -0.416802, -8.45734, 2.31239]
21 -0.330165 [0.0138814, 0.0275335, 0.0354732, -0.397741, -8.456, 2.2964]
22 -0.330498 [0.0125641, 0.027516, 0.0360846, -0.379656, -8.46291, 2.28086]
23 -0.330755 [0.0128642, 0.0278502, 0.0363866, -0.380687, -8.47017, 2.25698]
24 -0.330818 [0.013027, 0.0285871, 0.0364576, -0.38365, -8.47776, 2.2334]
25 -0.330765 [0.0132597, 0.0295509, 0.0365295, -0.373795, -8.47662, 2.21054]
26 -0.330542 [0.013672, 0.030487, 0.0362404, -0.364026, -8.47181, 2.18813]
27 -0.330322 [0.0141895, 0.0256162, 0.035576, -0.358216, -8.44983, 2.18495]
28 -0.330797 [0.0136179, 0.0269295, 0.0353163, -0.36477, -8.45458, 2.17588]
29 -0.330975 [0.0118522, 0.0283933, 0.0362561, -0.368978, -8.4648, 2.17279]
30 -0.331158 [0.0121628, 0.0285771, 0.0362582, -0.364078, -8.4666, 2.16145]
31 -0.331122 [0.0125626, 0.0288948, 0.0364175, -0.362397, -8.46578, 2.14914]
32 -0.331079 [0.0129816, 0.0294613, 0.0364742, -0.363751, -8.46328, 2.13705]
33 -0.330954 [0.0133428, 0.0301226, 0.0363145, -0.36287, -8.45831, 2.12572]
34 -0.330733 [0.0131618, 0.0304953, 0.035791, -0.372976, -8.45322, 2.12058]
35 -0.330706 [0.0122967, 0.030624, 0.0346822, -0.377635, -8.44197, 2.12061]
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252 -0.339452 [-0.00277437, 0.0281354, 0.0389676, -0.505781, -8.40358, 0.232358]
253 -0.339506 [-0.00288351, 0.0281423, 0.0390113, -0.508498, -8.40918, 0.232858]
254 -0.339532 [-0.00300278, 0.0282267, 0.0390442, -0.513182, -8.41329, 0.23324]
255 -0.339539 [-0.00310215, 0.0280509, 0.039292, -0.515059, -8.4192, 0.232802]
256 -0.339568 [-0.00320779, 0.028096, 0.0392385, -0.520393, -8.42242, 0.232352]
257 -0.339587 [-0.00320265, 0.0279718, 0.0392357, -0.525167, -8.42639, 0.232993]
258 -0.339621 [-0.00332199, 0.0279436, 0.0393374, -0.531042, -8.42849, 0.233098]
259 -0.339647 [-0.00342028, 0.0280775, 0.0394939, -0.536916, -8.43052, 0.23258]
Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 260 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.995304 -0.0790866 0.0558185
0.0787025 0.996857 0.00905027
-0.0563588 -0.00461472 0.9984
Offset = [0.0297227, -8.38772, 0.251226]
=============================== Starting Transform Estimations for ScaleSkewVersor3D(2 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1].
0 -0.339341 [-0.00104292, 0.0123065, 0.0354632, -0.52825, -8.30837, 0.119532, 0.927847, 0.942225, 0.954708, 0.0107369, -0.0110698, -0.0040957, 0.00727432, 0.0120789, 0.00962651]
1 -0.421061 [-0.00120642, 0.0157551, 0.0346184, -0.451239, -8.35885, 0.0843825, 0.927747, 0.929825, 0.947316, 0.0122861, -0.00642601, -0.00426722, 0.00723992, 0.0134403, 0.00937264]
2 -0.438847 [-0.0025459, 0.0181027, 0.0326432, -0.400335, -8.43969, 0.0600056, 0.928777, 0.916259, 0.942701, 0.0153165, -0.00302123, -0.00403882, 0.00610573, 0.0144325, 0.00685172]
3 -0.456946 [-0.00299921, 0.0186466, 0.0318457, -0.36053, -8.5301, 0.05557, 0.930191, 0.903113, 0.938658, 0.0162169, -0.00125778, -0.0045904, 0.00319958, 0.0155265, 0.00351252]
4 -0.47003 [-0.00375003, 0.0216937, 0.0303227, -0.32404, -8.60546, 0.108404, 0.93449, 0.893723, 0.93904, 0.017302, 0.00144253, -0.0052006, -0.000510782, 0.0147175, -0.000838293]
5 -0.479342 [-0.0044592, 0.0231841, 0.0299225, -0.243121, -8.62646, 0.162027, 0.940527, 0.887305, 0.935754, 0.0165985, 0.00207934, -0.0061632, -0.00426329, 0.0134827, -0.00511914]
6 -0.482398 [-0.00399372, 0.0224424, 0.0304488, -0.167505, -8.60958, 0.225136, 0.943203, 0.88801, 0.93565, 0.0153044, 0.00159743, -0.0067326, -0.00428109, 0.013661, -0.00465892]
7 -0.482892 [-0.00364976, 0.0236838, 0.029698, -0.100977, -8.59284, 0.297714, 0.944169, 0.88782, 0.932428, 0.0151165, 0.00355599, -0.00757408, -0.00504179, 0.0144556, -0.00505453]
8 -0.481982 [-0.00400288, 0.0219785, 0.0314504, -0.0535731, -8.58837, 0.385397, 0.945194, 0.889404, 0.935396, 0.0138677, 0.00127403, -0.00694081, -0.00483743, 0.013688, -0.00522368]
9 -0.482881 [-0.000933667, 0.0248589, 0.031333, 0.0440169, -8.57646, 0.398858, 0.94235, 0.88434, 0.930688, 0.0143972, 0.00544869, -0.006949, -0.0057258, 0.0154465, -0.00306985]
10 -0.47935 [-0.00322625, 0.0224189, 0.0309996, 0.0511006, -8.56591, 0.497355, 0.945883, 0.888502, 0.935751, 0.0151524, 0.000813019, -0.00605081, -0.00590485, 0.0126721, -0.00543561]
11 -0.482706 [-0.00289073, 0.0255071, 0.0321389, 0.0979344, -8.55928, 0.485349, 0.944065, 0.884971, 0.930168, 0.0138785, 0.00545437, -0.00649564, -0.00553914, 0.0146046, -0.0047713]
12 -0.480763 [-0.00304888, 0.0245943, 0.0319424, 0.099875, -8.55307, 0.509315, 0.94447, 0.885767, 0.931246, 0.014137, 0.0039847, -0.00636518, -0.00558342, 0.0139594, -0.00495067]
13 -0.481995 [-0.00323976, 0.0242162, 0.03191, 0.104069, -8.54975, 0.533693, 0.944776, 0.886081, 0.931967, 0.0141926, 0.00329112, -0.00630292, -0.00567883, 0.0135755, -0.00522297]
14 -0.482486 [-0.00346022, 0.0239542, 0.0317319, 0.105443, -8.54415, 0.557991, 0.94491, 0.886169, 0.932375, 0.0143463, 0.00272666, -0.00631566, -0.00572734, 0.0132296, -0.00547349]
15 -0.482673 [-0.00366325, 0.0240397, 0.0315223, 0.106213, -8.53874, 0.582369, 0.944933, 0.886173, 0.932491, 0.0144844, 0.00233292, -0.00639102, -0.00569345, 0.0127333, -0.00560893]
16 -0.482735 [-0.00355593, 0.0240675, 0.0315693, 0.113346, -8.53034, 0.604796, 0.944768, 0.886007, 0.932194, 0.0141942, 0.00194293, -0.00666064, -0.00565477, 0.0123503, -0.00542194]
17 -0.482628 [-0.00394154, 0.0249342, 0.0313117, 0.11557, -8.52543, 0.629117, 0.94479, 0.886021, 0.931933, 0.0144563, 0.00235419, -0.00666232, -0.00541314, 0.0118958, -0.00553558]
18 -0.482497 [-0.00388508, 0.0245055, 0.0312564, 0.127748, -8.51808, 0.649651, 0.944797, 0.885962, 0.931902, 0.0145999, 0.00191792, -0.00657696, -0.00550475, 0.0118867, -0.00557374]
19 -0.482563 [-0.00385954, 0.0240469, 0.0314339, 0.145942, -8.51012, 0.664794, 0.94478, 0.885901, 0.931866, 0.0143122, 0.00156116, -0.00670238, -0.00535552, 0.0120045, -0.00539926]
20 -0.482594 [-0.00398192, 0.0244919, 0.0311569, 0.152674, -8.50292, 0.687735, 0.944956, 0.886077, 0.931749, 0.0145286, 0.00207766, -0.00674011, -0.00528366, 0.012068, -0.00545217]
21 -0.482511 [-0.00432533, 0.023682, 0.0315173, 0.167141, -8.49912, 0.707634, 0.944474, 0.885669, 0.931322, 0.0141591, 0.00128184, -0.00680088, -0.00550319, 0.0120954, -0.00600797]
22 -0.482465 [-0.00417815, 0.0239793, 0.0312789, 0.175758, -8.49114, 0.729663, 0.944796, 0.885947, 0.931142, 0.0146922, 0.00187462, -0.006467, -0.00540649, 0.0123937, -0.00579854]
23 -0.482436 [-0.00402283, 0.0236311, 0.0314935, 0.180674, -8.48739, 0.753868, 0.944833, 0.885911, 0.931034, 0.0145529, 0.00171779, -0.00638466, -0.00557431, 0.0125885, -0.00582571]
24 -0.482337 [-0.00410565, 0.024075, 0.0312223, 0.185744, -8.4821, 0.777726, 0.944858, 0.885944, 0.930963, 0.0151939, 0.00230725, -0.00601332, -0.00541311, 0.012735, -0.00577378]
25 -0.482243 [-0.00359935, 0.0228886, 0.0322967, 0.188839, -8.48302, 0.80216, 0.944568, 0.884654, 0.930185, 0.0136303, 0.00171179, -0.00657743, -0.00600397, 0.0133853, -0.00585474]
26 -0.481927 [-0.00422602, 0.0234958, 0.0316167, 0.18563, -8.475, 0.825427, 0.945092, 0.885993, 0.930208, 0.0147836, 0.00205448, -0.00600529, -0.00547712, 0.0130802, -0.00596987]
27 -0.48203 [-0.00405032, 0.023685, 0.0315596, 0.180251, -8.45897, 0.843805, 0.945073, 0.885383, 0.930338, 0.015254, 0.00256188, -0.00561992, -0.00561982, 0.0133903, -0.0059715]
28 -0.482052 [-0.00398132, 0.0226793, 0.0328855, 0.175045, -8.43548, 0.849289, 0.944765, 0.885534, 0.929314, 0.0138105, 0.00173118, -0.00577637, -0.00511861, 0.0136755, -0.00540237]
29 -0.481696 [-0.00544996, 0.0243649, 0.0306223, 0.164708, -8.43564, 0.870618, 0.946331, 0.887533, 0.931541, 0.0165617, 0.00291058, -0.00506874, -0.0046255, 0.0129104, -0.00639673]
30 -0.481655 [-0.00547443, 0.0239544, 0.0312822, 0.161796, -8.43758, 0.859133, 0.945412, 0.885695, 0.929733, 0.0154276, 0.00221604, -0.00571395, -0.00475612, 0.0127654, -0.00647166]
31 -0.481965 [-0.00555346, 0.023744, 0.0315213, 0.16649, -8.43604, 0.862874, 0.945319, 0.885542, 0.929574, 0.0151373, 0.00194389, -0.00578106, -0.00480903, 0.012711, -0.00659373]
32 -0.482017 [-0.00562035, 0.0236249, 0.0316886, 0.17083, -8.43376, 0.866712, 0.945275, 0.88546, 0.92943, 0.0149416, 0.00178652, -0.00581609, -0.00487314, 0.0126756, -0.00671842]
33 -0.482033 [-0.00560718, 0.0235589, 0.0317878, 0.175508, -8.43117, 0.869929, 0 |
|
|
for some reason the note got cut off where it got interesting :
34 -0.482011 [-0.00559201, 0.0235203, 0.0319117, 0.180203, -8.42878, 0.873278, 0.945145, 0.885262, 0.929231, 0.0146916, 0.00159369, -0.00586157, -0.00496297, 0.012602, -0.00676864]
35 -0.48195 [-0.00564387, 0.0235059, 0.0320234, 0.184649, -8.42665, 0.877106, 0.94508, 0.885198, 0.929116, 0.0146038, 0.00156943, -0.00584655, -0.00495206, 0.012599, -0.00680813]
36 -0.481914 [-0.00563944, 0.0235103, 0.0321162, 0.189375, -8.42502, 0.88085, 0.94506, 0.88518, 0.929074, 0.0145245, 0.00153873, -0.00583574, -0.00494866, 0.0125682, -0.00679812]
37 -0.481901 [-0.00565849, 0.0234729, 0.0321792, 0.193949, -8.42322, 0.884701, 0.94501, 0.885141, 0.928973, 0.0144701, 0.00145073, -0.00583392, -0.00494719, 0.0125243, -0.00681134]
38 -0.481866 [-0.00562817, 0.0234925, 0.0323099, 0.198134, -8.42153, 0.889016, 0.944939, 0.885119, 0.928876, 0.0143952, 0.00144249, -0.00578352, -0.00495791, 0.0125063, -0.00679145]
39 -0.481805 [-0.00564865, 0.0234865, 0.0323728, 0.20216, -8.42074, 0.893727, 0.944875, 0.885157, 0.928857, 0.0143714, 0.00144866, -0.00574802, -0.00490949, 0.0125243, -0.00676648]
40 -0.481806 [-0.00568009, 0.0234592, 0.0324618, 0.206925, -8.42023, 0.897733, 0.944786, 0.885182, 0.928836, 0.0143174, 0.00142956, -0.00571855, -0.00487825, 0.0125381, -0.00676898]
41 -0.481808 [-0.00574734, 0.0234576, 0.0325106, 0.210624, -8.41931, 0.902679, 0.944636, 0.88509, 0.928771, 0.0143168, 0.00141204, -0.005687, -0.00486293, 0.0125289, -0.00682019]
42 -0.481786 [-0.00577278, 0.0234129, 0.0325182, 0.214349, -8.41788, 0.907486, 0.944575, 0.885013, 0.92865, 0.0143435, 0.00134177, -0.00566436, -0.00482158, 0.0125128, -0.00680199]
43 -0.481751 [-0.00580852, 0.0233854, 0.0325427, 0.218198, -8.41697, 0.912322, 0.944484, 0.884979, 0.928628, 0.0143573, 0.00123519, -0.00563704, -0.00479086, 0.0124388, -0.0068029]
44 -0.481744 [-0.0058365, 0.0233161, 0.0325906, 0.222614, -8.41593, 0.916614, 0.944395, 0.88497, 0.928608, 0.0143313, 0.00113163, -0.00562419, -0.00475931, 0.0124103, -0.00679777]
45 -0.481754 [-0.00585884, 0.0233606, 0.0325703, 0.225697, -8.41449, 0.921849, 0.944199, 0.884892, 0.928489, 0.0143891, 0.00109477, -0.00560655, -0.00472582, 0.012344, -0.00678079]
46 -0.48173 [-0.00585057, 0.0233517, 0.0325245, 0.22914, -8.4126, 0.926705, 0.94411, 0.884902, 0.928418, 0.0144576, 0.000974003, -0.00559035, -0.00473326, 0.0122392, -0.00677307]
47 -0.481669 [-0.00593407, 0.0234061, 0.0325596, 0.232306, -8.41106, 0.931862, 0.944026, 0.884909, 0.92836, 0.0144363, 0.000993988, -0.00558036, -0.00475108, 0.0122051, -0.00687215]
48 -0.481672 [-0.00598646, 0.0234181, 0.0325059, 0.235238, -8.40921, 0.937058, 0.943994, 0.884869, 0.928209, 0.0144973, 0.000964563, -0.00557923, -0.00473161, 0.0121695, -0.00690047]
49 -0.48163 [-0.00602727, 0.0234418, 0.0324598, 0.23861, -8.40712, 0.941885, 0.943977, 0.884861, 0.928152, 0.0145378, 0.00093013, -0.00558733, -0.00472449, 0.0121124, -0.0069293]
50 -0.481578 [-0.00599473, 0.0234587, 0.0325103, 0.242404, -8.4049, 0.946324, 0.943993, 0.884897, 0.9281, 0.0144704, 0.000877245, -0.00560181, -0.00471641, 0.0120479, -0.00688341]
51 -0.481546 [-0.00599809, 0.0235137, 0.0324431, 0.245579, -8.40282, 0.951285, 0.944021, 0.88494, 0.928066, 0.0145157, 0.000923723, -0.00561901, -0.00470787, 0.0120395, -0.00687686]
52 -0.481512 [-0.00597135, 0.0235382, 0.0325001, 0.24862, -8.40071, 0.95632, 0.944106, 0.884915, 0.928045, 0.014449, 0.000905185, -0.00562633, -0.00467909, 0.0119978, -0.00681766]
53 -0.481485 [-0.0060583, 0.0235577, 0.0325492, 0.251115, -8.39904, 0.961794, 0.944139, 0.88497, 0.928049, 0.0143945, 0.000895497, -0.00562662, -0.00466542, 0.0119626, -0.00688944]
54 -0.48153 [-0.00620281, 0.0236122, 0.0325454, 0.253861, -8.39822, 0.967332, 0.944146, 0.8849, 0.927899, 0.0143727, 0.000800344, -0.00565598, -0.00470185, 0.0118086, -0.00705655]
55 -0.481472 [-0.00636826, 0.0238238, 0.0325838, 0.258266, -8.397, 0.971552, 0.944255, 0.884819, 0.927846, 0.0143896, 0.000817039, -0.00560164, -0.00463855, 0.0116042, -0.00714672]
56 -0.481498 [-0.00654699, 0.0239606, 0.032671, 0.260827, -8.39715, 0.977226, 0.944298, 0.884871, 0.927909, 0.0143423, 0.000878803, -0.00556154, -0.00448666, 0.0115226, -0.00717193]
57 -0.481573 [-0.00672658, 0.0240622, 0.0329324, 0.261904, -8.39694, 0.983336, 0.944353, 0.884919, 0.92802, 0.0141726, 0.000879105, -0.00546777, -0.0043719, 0.0114108, -0.00723646]
58 -0.481628 [-0.00676574, 0.02394, 0.0329673, 0.257358, -8.39825, 0.987401, 0.944442, 0.884992, 0.927974, 0.0141194, 0.000778968, -0.00548466, -0.00420997, 0.0114397, -0.00711487]
59 -0.481644 [-0.00699861, 0.0242342, 0.0333311, 0.252603, -8.40119, 0.98995, 0.94453, 0.885108, 0.928167, 0.0138396, 0.000958624, -0.00539146, -0.00404394, 0.01131, -0.00718235]
60 -0.481697 [-0.00698262, 0.0238404, 0.0331569, 0.247072, -8.40284, 0.987824, 0.944897, 0.885081, 0.927917, 0.0139925, 0.00105837, -0.00539276, -0.00396677, 0.0118015, -0.00711743]
61 -0.481648 [-0.00700706, 0.0240518, 0.0331762, 0.243808, -8.40718, 0.984792, 0.945034, 0.88504, 0.928235, 0.0139524, 0.00108692, -0.0054101, -0.00389341, 0.0116007, -0.00705884]
62 -0.481705 [-0.00628858, 0.0240521, 0.0335483, 0.237996, -8.40785, 0.98411, 0.945728, 0.884088, 0.928274, 0.0137088, 0.00116681, -0.00527409, -0.00437558, 0.0116638, -0.00682096]
63 -0.481581 [-0.00751771, 0.023838, 0.0332564, 0.233969, -8.40838, 0.987658, 0.946178, 0.885438, 0.927997, 0.0137363, 0.0015557, -0.00543818, -0.00383794, 0.0122098, -0.00755417]
Stop condition from optimizer.VersorTransformOptimizer: Step too small after 64 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.94283 -0.0530774 0.0486903
0.0606586 0.883113 0.01277
-0.0359249 -0.020991 0.926747
Offset = [0.722479, -8.13372, 0.476154]
=============================== Starting Transform Estimations for Affine(3 of 4).===============================
Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001].
0 -0.478939 [0.94963, -0.0421173, 0.0355271, 0.0631961, 0.875416, 0.00331817, -0.03367, -0.0131815, 0.933877, 0.358352, -8.40584, 1.14229]
1 -0.475657 [0.944263, -0.0461503, 0.0400121, 0.0601327, 0.876511, 0.00488964, -0.0301118, -0.012659, 0.927026, 0.402444, -8.39554, 1.05391]
2 -0.478597 [0.945397, -0.048433, 0.0415655, 0.0589979, 0.884713, 0.00299965, -0.0285623, -0.0171957, 0.927219, 0.43063, -8.37822, 1.08998]
3 -0.478771 [0.944095, -0.0489188, 0.0420445, 0.0584015, 0.882304, 0.00403349, -0.0284068, -0.0153513, 0.925743, 0.418204, -8.37877, 1.06865]
4 -0.478549 [0.944497, -0.0491893, 0.0421221, 0.0582383, 0.882471, 0.0042847, -0.0287133, -0.0152283, 0.926308, 0.411255, -8.37696, 1.07884]
5 -0.478795 [0.944504, -0.0491235, 0.0424095, 0.0581455, 0.882503, 0.00449243, -0.0287461, -0.0153678, 0.92647, 0.401904, -8.37182, 1.08534]
6 -0.478804 [0.944651, -0.0489694, 0.0424213, 0.0580727, 0.882386, 0.00491657, -0.0291732, -0.0155698, 0.926392, 0.391621, -8.36514, 1.08768]
7 -0.478789 [0.944711, -0.0488706, 0.0428515, 0.057962, 0.882388, 0.00545569, -0.0294267, -0.0158095, 0.926133, 0.388687, -8.36153, 1.09925]
8 -0.478708 [0.944892, -0.049358, 0.0427129, 0.0578203, 0.882448, 0.00589834, -0.0294996, -0.0155552, 0.926707, 0.398903, -8.35779, 1.10533]
9 -0.478875 [0.944678, -0.0491629, 0.0426447, 0.0579268, 0.882334, 0.00584711, -0.0296695, -0.0155947, 0.926298, 0.397716, -8.35261, 1.10209]
10 -0.478796 [0.944506, -0.049133, 0.0425233, 0.0579554, 0.882121, 0.0057473, -0.0296619, -0.0155945, 0.926322, 0.401555, -8.34829, 1.10445]
11 -0.478787 [0.944507, -0.0492291, 0.0425117, 0.0578671, 0.882068, 0.00573225, -0.0296482, -0.0157644, 0.926272, 0.406362, -8.34553, 1.10732]
12 -0.478784 [0.944489, -0.0492543, 0.0424871, 0.0578482, 0.882097, 0.00581169, -0.0296448, -0.0157827, 0.926509, 0.410731, -8.34162, 1.10947]
13 -0.478762 [0.944355, -0.049335, 0.0425258, 0.05773, 0.881958, 0.00568978, -0.0295882, -0.0159259, 0.926415, 0.414295, -8.33661, 1.10843]
14 -0.478744 [0.944501, -0.0492945, 0.0425418, 0.0576856, 0.882036, 0.00562856, -0.0296589, -0.0160389, 0.926661, 0.414332, -8.33259, 1.1132]
15 -0.4788 [0.94426, -0.0494357, 0.042723, 0.0575313, 0.881756, 0.00555116, -0.0297205, -0.0161693, 0.926306, 0.414931, -8.32646, 1.11411]
16 -0.478669 [0.944345, -0.0494594, 0.0427164, 0.0575025, 0.881958, 0.00572391, -0.0297664, -0.015975, 0.926655, 0.417834, -8.32333, 1.11865]
17 -0.478735 [0.944168, -0.0494544, 0.0427441, 0.0574572, 0.881993, 0.00577724, -0.0298158, -0.0162588, 0.926046, 0.41776, -8.31721, 1.1197]
18 -0.478587 [0.944339, -0.0495245, 0.0427544, 0.0574824, 0.882203, 0.00589885, -0.0298329, -0.0160401, 0.926599, 0.420645, -8.31395, 1.12413]
19 -0.478735 [0.944143, -0.0497683, 0.0426587, 0.0573868, 0.88199, 0.00582653, -0.0300221, -0.0160975, 0.926342, 0.421968, -8.30905, 1.12052]
Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005).
Matrix =
0.944143 -0.0497683 0.0426587
0.0573868 0.88199 0.00582653
-0.0300221 -0.0160975 0.926342
Offset = [0.857941, -8.08442, 0.595072]
=============================== Starting Transform Estimations for BSpline(4 of 4).===============================
Starting Registration
Probe Tag Starts Stops Time (s)
Registration 1 1 297.418
Stop condition from optimizer.LBFGSBOptimizer: Function tolerance reached after 81 iterations. The relative reduction of the cost function <= 2.22045e-07 = CostFunctionConvergenceFactor (1e+09) * machine precision (2.22045e-16).
TCL: ReadDataFromDisk: Try to read /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn13405259232cIAeZ_vtkMRMLScalarVolumeNode16.nrrd
TCL: ReadDataFromDisk: Try to read /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn968247184XIDPJB_vtkMRMLBSplineTransformNode1.mat
TCL: RegisterAtlas: calcDFVolumeNode START
TCL: ==========================================
TCL: == Create deformation field
TCL: ==========================================
TCL: Create file: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn1846828169pWbKNm_vtkMRMLBSplineTransformNode1.mat
TCL: Create file: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn2059886292u2FvgC_vtkMRMLScalarVolumeNode7.nrrd
TCL: Create file: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn925036357IwXdJi_vtkMRMLScalarVolumeNode10.nrrd
TCL: Create file: /var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn1451931466AvjtvT_vtkMRMLScalarVolumeNode17.nrrd
TCL: Executing /Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/cli-modules//BSplineToDeformationField --refImage "/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn925036357IwXdJi_vtkMRMLScalarVolumeNode10.nrrd" --tfm "/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn1846828169pWbKNm_vtkMRMLBSplineTransformNode1.mat" --defImage "/var/folders/13/ctgvj7r144vgzlpl_11k_wfr0000gp/T/Slicer/fn1451931466AvjtvT_vtkMRMLScalarVolumeNode17.nrrd"
Error executing __tpycl_result = slicer.OOlYZLPp.PrintText('TCL: ---- couldn't execute "/Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/cli-modules/BSplineToDeformationField": no such file or directory ----')
(<type 'exceptions.SyntaxError'>, SyntaxError('invalid syntax', ('<string>', 1, 62, '__tpycl_result = slicer.OOlYZLPp.PrintText(\'TCL: ---- couldn\'t execute "/Users/rkikinis/Downloads/Slicer-4.0.gamma-2011-11-09-macosx-amd64.app/Contents/cli-modules/BSplineToDeformationField": no such file or directory ----\')')), <traceback object at 0x134f287a0>)
while executing
"py_eval $pycmd" |
