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IDProjectCategoryView StatusDate SubmittedLast Update
0004315Slicer4Core: Diffusion and Tractography (Any modules)public2016-12-09 09:362017-06-09 10:30
Reporterhjmjohnson Assigned Toinorton  
PriorityhighSeveritymajorReproducibilityalways
Status closedResolutionfixed 
PlatformOSMacOS Version10.12
Product VersionSlicer 4.7.0 
Target VersionSlicer 4.7.0Fixed in Version 
Summary0004315: Diffusion Tools not working in Slicer 4.6.2 or 4.7.0
Description

There appears to be a problem with external tools for processing DWI data.

It appears that the diffussion command line tools are not passing nodes from slicer to the CLI based tools.

The tools work great when run from the command line. This is happening in both 4.6.2 and today's nightly.

The following works great from the command line
DWIIN=DicomToNrrdGeSignaHDx.nhdr
DTIOUT=SlicerTest_DTI.nrrd
BASELINEOUT=${DWIIN//.nhdr/_Baseline.nrrd}

/Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/cli-modules/DWIToDTIEstimation \
--enumeration LS ${DWIIN} ${DTIOUT} ${BASELINEOUT}

Steps To Reproduce

Load DWI nrrd image, try to convert to tensor image.

Write: Error wrapping nrrd for /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLScalarVolumeNodeD.nrrd:
[nrrd] nrrdWrap_nva:
[nrrd] _nrrdSizeCheck: axis 1 size is zero!

Additional Information

cat /Users/johnsonhj/Slicer/data/Slicer_25603_20161209_080435.log

[DEBUG][Qt] 09.12.2016 08:04:35 [] (unknown:0) - Session start time .......: 2016-12-09 08:04:35
[DEBUG][Qt] 09.12.2016 08:04:35 [] (unknown:0) - Slicer version ...........: 4.7.0-2016-12-08 (revision 25603) macosx-amd64 - installed
[DEBUG][Qt] 09.12.2016 08:04:35 [] (unknown:0) - Operating system .........: Mac OS X / 10.12.1 / 16B2555 - 64-bit
[DEBUG][Qt] 09.12.2016 08:04:35 [] (unknown:0) - Memory ...................: 16384 MB physical, 1024 MB virtual
[DEBUG][Qt] 09.12.2016 08:04:35 [] (unknown:0) - CPU ......................: GenuineIntel Intel(R) Core(TM) i7-4578U CPU @ 3.00GHz, 2 cores, 4 logical processors
[DEBUG][Qt] 09.12.2016 08:04:35 [] (unknown:0) - Developer mode enabled ...: no
[DEBUG][Qt] 09.12.2016 08:04:35 [] (unknown:0) - Prefer executable CLI ....: no
[DEBUG][Qt] 09.12.2016 08:04:35 [] (unknown:0) - Additional module paths ..: /Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/cli-modules, /Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/qt-loadable-modules, /Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/qt-scripted-modules, /Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/UKFTractography/lib/Slicer-4.7/cli-modules
[DEBUG][Qt] 09.12.2016 08:04:37 [] (unknown:0) - Number of registered modules: 150
[DEBUG][Qt] 09.12.2016 08:04:38 [] (unknown:0) - Number of instantiated modules: 150
[WARNING][Qt] 09.12.2016 08:04:38 [] (unknown:0) - When loading module "CLIEventTest" , the dependency "CLI4Test" failed to be loaded.
[INFO][Stream] 09.12.2016 08:04:41 [] (unknown:0) - Initializing terminology mapping for map file /Users/johnsonhj/Desktop/Slicer.app/Contents/share/Slicer-4.7/ColorFiles/Terminology//GenericAnatomyColors-SNOMED.csv
[INFO][Stream] 09.12.2016 08:04:41 [] (unknown:0) - 288 terms were read for Slicer LUT GenericAnatomyColors
[WARNING][Qt] 09.12.2016 08:04:41 [] (unknown:0) - Failed to retrieve module title corresponding to module name: "DMRIInstall"
[INFO][VTK] 09.12.2016 08:04:41 [vtkSlicerTerminologiesModuleLogic (0x123b50ad0)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologiesModuleLogic.cxx:893) - Terminology named 'Segmentation category and type - 3D Slicer General Anatomy list' successfully loaded from file /Users/johnsonhj/Desktop/Slicer.app/Contents/share/Slicer-4.7/qt-loadable-modules/Terminologies/SegmentationCategoryTypeModifier-SlicerGeneralAnatomy.json
[INFO][VTK] 09.12.2016 08:04:41 [vtkSlicerTerminologiesModuleLogic (0x123b50ad0)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologiesModuleLogic.cxx:893) - Terminology named 'Segmentation category and type - DICOM master list' successfully loaded from file /Users/johnsonhj/Desktop/Slicer.app/Contents/share/Slicer-4.7/qt-loadable-modules/Terminologies/SegmentationCategoryTypeModifier-DICOM-Master.json
[INFO][VTK] 09.12.2016 08:04:42 [vtkSlicerTerminologiesModuleLogic (0x123b50ad0)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologiesModuleLogic.cxx:968) - Anatomic context named 'Anatomic codes - DICOM master list' successfully loaded from file /Users/johnsonhj/Desktop/Slicer.app/Contents/share/Slicer-4.7/qt-loadable-modules/Terminologies/AnatomicRegionModifier-Master.json
[WARNING][Qt] 09.12.2016 08:04:42 [] (unknown:0) - When loading module "TwoCLIsInARowTest" , the dependency "CLI4Test" failed to be loaded.
[WARNING][Qt] 09.12.2016 08:04:42 [] (unknown:0) - When loading module "TwoCLIsInParallelTest" , the dependency "CLI4Test" failed to be loaded.
[DEBUG][Qt] 09.12.2016 08:04:42 [] (unknown:0) - Number of loaded modules: 147
[DEBUG][Qt] 09.12.2016 08:04:42 [] (unknown:0) - Switch to module: "Welcome"
[INFO][VTK] 09.12.2016 08:04:45 [vtkMRMLVolumeArchetypeStorageNode (0x12d8be920)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:456) - Loaded volume from file: /Users/johnsonhj/src/BT-11/BRAINSTools-build/DWIConvert/test99/GeSignaHDx/DicomToNrrdGeSignaHDx_DTI.nhdr. Dimensions: 256x256x44. Number of components: 1. Pixel type: double.
[ERROR][VTK] 09.12.2016 08:04:45 [vtkMRMLSceneViewStorageNode (0x11afd32e0)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Libs/MRML/Core/vtkMRMLSceneViewStorageNode.cxx:86) - ReadDataInternal: file does not exist: /Users/johnsonhj/src/BT-11/BRAINSTools-build/DWIConvert/test99/GeSignaHDx/Master Scene View.png
[INFO][VTK] 09.12.2016 08:04:45 [vtkMRMLVolumeArchetypeStorageNode (0x12d65aa70)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:456) - Loaded volume from file: /Users/johnsonhj/src/BT-11/BRAINSTools-build/DWIConvert/test99/GeSignaHDx/DicomToNrrdGeSignaHDx_FA.nrrd. Dimensions: 256x256x44. Number of components: 1. Pixel type: unsigned short.
[INFO][Stream] 09.12.2016 08:04:45 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:04:45 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:04:45 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:04:45 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[DEBUG][Qt] 09.12.2016 08:04:45 [] (unknown:0) - "Volume" Reader has successfully read the file "DicomToNrrdGeSignaHDx_FA.nrrd" "[0.16s]"
[INFO][VTK] 09.12.2016 08:04:45 [vtkMRMLVolumeArchetypeStorageNode (0x12cfd8f00)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:456) - Loaded volume from file: /Users/johnsonhj/src/BT-11/BRAINSTools-build/DWIConvert/test99/GeSignaHDx/DicomToNrrdGeSignaHDx_MD.nrrd. Dimensions: 256x256x44. Number of components: 1. Pixel type: unsigned short.
[INFO][Stream] 09.12.2016 08:04:45 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:04:45 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[DEBUG][Qt] 09.12.2016 08:04:45 [] (unknown:0) - "Volume" Reader has successfully read the file "DicomToNrrdGeSignaHDx_MD.nrrd" "[0.10s]"
[DEBUG][Qt] 09.12.2016 08:05:01 [] (unknown:0) - Switch to module: "DWIToDTIEstimation"
[CRITICAL][FD] 09.12.2016 08:05:19 [] (unknown:0) - 2016-12-09 08:05:19.907 Slicer[30546:2021700] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[DEBUG][Qt] 09.12.2016 08:05:22 [] (unknown:0) - Found CommandLine Module, target is /Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/cli-modules/DWIToDTIEstimation
[DEBUG][Qt] 09.12.2016 08:05:22 [] (unknown:0) - ModuleType: CommandLineModule
[ERROR][VTK] 09.12.2016 08:05:22 [vtkSlicerCLIModuleLogic (0x12045ce90)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Base/QTCLI/vtkSlicerCLIModuleLogic.cxx:1882) - No output data assigned to "Output Baseline Volume"
[ERROR][VTK] 09.12.2016 08:05:38 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:38 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:38 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:38 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:40 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:40 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:40 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:40 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:43 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:43 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:43 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:43 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:44 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:44 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:44 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:44 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:47 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:47 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:47 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:47 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:52 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:52 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:52 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:52 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[CRITICAL][FD] 09.12.2016 08:05:52 [] (unknown:0) - 2016-12-09 08:05:52.867 Slicer[30546:2021700] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[ERROR][VTK] 09.12.2016 08:05:55 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:55 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:55 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:05:55 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:00 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:00 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:00 [vtkCompositeDataPipeline (0x12e0ad940)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0ac190) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:00 [vtkCompositeDataPipeline (0x12e0cf320)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0acd50) has 0 connections but is not optional.
[CRITICAL][FD] 09.12.2016 08:06:00 [] (unknown:0) - 2016-12-09 08:06:00.122 Slicer[30546:2021700] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[DEBUG][Qt] 09.12.2016 08:06:02 [] (unknown:0) - Found CommandLine Module, target is /Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/cli-modules/DWIToDTIEstimation
[DEBUG][Qt] 09.12.2016 08:06:02 [] (unknown:0) - ModuleType: CommandLineModule
[DEBUG][Qt] 09.12.2016 08:06:03 [] (unknown:0) - Diffusion Tensor Estimation command line:

/Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/cli-modules/DWIToDTIEstimation --enumeration LS /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLDiffusionTensorVolumeNodeC.nrrd /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLScalarVolumeNodeD.nrrd
[ERROR][VTK] 09.12.2016 08:06:03 [vtkNRRDWriter (0x10ad43560)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Base/QTCLI/vtkSlicerCLIModuleLogic.cxx, line 2147
vtkSlicerCLIModuleLogic (0x12045ce90): Diffusion Tensor Estimation standard error:

ERROR: In /Users/kitware/Dashboards/Nightly/S-0-E-b/SlicerDMRI/Libs/vtkDMRI/vtkTeemEstimateDiffusionTensor.cxx, line 272
vtkTeemEstimateDiffusionTensor (0x10ad366b0): The input has to have a number of components equal to the number of gradients

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkExecutive.cxx, line 784
vtkCompositeDataPipeline (0x10ad37d90): Algorithm vtkTeemEstimateDiffusionTensor(0x10ad366b0) returned failure for request: vtkInformation (0x10ad3d990)
Debug: Off
Modified Time: 563
Reference Count: 1
Registered Events: (none)
Request: REQUEST_DATA
FORWARD_DIRECTION: 0
FROM_OUTPUT_PORT: 0
ALGORITHM_AFTER_FORWARD: 1

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0/Libs/vtkTeem/vtkNRRDWriter.cxx, line 243
vtkNRRDWriter (0x10ad3f480): Write: Error wrapping nrrd for /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLDiffusionTensorVolumeNodeC.nrrd:
[nrrd] nrrdWrap_nva:
[nrrd] _nrrdSizeCheck: axis 0 size is zero!

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0/Libs/vtkTeem/vtkNRRDWriter.cxx:243) - Write: Error wrapping nrrd for /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLScalarVolumeNodeD.nrrd:
[nrrd] nrrdWrap_nva:
[nrrd] _nrrdSizeCheck: axis 0 size is zero!
[DEBUG][Qt] 09.12.2016 08:06:03 [] (unknown:0) - Diffusion Tensor Estimation completed without errors
[INFO][Stream] 09.12.2016 08:06:03 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:06:03 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[ERROR][VTK] 09.12.2016 08:06:03 [vtkCompositeDataPipeline (0x12de289e0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12de27e10) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:03 [vtkCompositeDataPipeline (0x12de2e820)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageThreshold(0x12de0dd90) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:03 [vtkCompositeDataPipeline (0x12de289e0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12de27e10) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:03 [vtkCompositeDataPipeline (0x12de289e0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12de27e10) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:03 [vtkCompositeDataPipeline (0x12de2e820)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageThreshold(0x12de0dd90) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:03 [vtkCompositeDataPipeline (0x12de289e0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12de27e10) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:05 [vtkCompositeDataPipeline (0x12de289e0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12de27e10) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:05 [vtkCompositeDataPipeline (0x12de2e820)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageThreshold(0x12de0dd90) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:05 [vtkCompositeDataPipeline (0x12de289e0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12de27e10) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:05 [vtkCompositeDataPipeline (0x12de289e0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12de27e10) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:05 [vtkCompositeDataPipeline (0x12de2e820)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageThreshold(0x12de0dd90) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:05 [vtkCompositeDataPipeline (0x12de289e0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12de27e10) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:06 [vtkCompositeDataPipeline (0x13cf46240)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf3fa20) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:06 [vtkCompositeDataPipeline (0x13cf111b0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf456b0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:06 [vtkCompositeDataPipeline (0x13cf46240)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf3fa20) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:06 [vtkCompositeDataPipeline (0x13cf111b0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf456b0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:11 [vtkCompositeDataPipeline (0x13cf46240)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf3fa20) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:11 [vtkCompositeDataPipeline (0x13cf111b0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf456b0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:11 [vtkCompositeDataPipeline (0x13cf46240)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf3fa20) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:11 [vtkCompositeDataPipeline (0x13cf111b0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf456b0) has 0 connections but is not optional.
[DEBUG][Qt] 09.12.2016 08:06:15 [] (unknown:0) - Found CommandLine Module, target is /Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/cli-modules/DWIToDTIEstimation
[DEBUG][Qt] 09.12.2016 08:06:15 [] (unknown:0) - ModuleType: CommandLineModule
[DEBUG][Qt] 09.12.2016 08:06:15 [] (unknown:0) - Diffusion Tensor Estimation command line:

/Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/cli-modules/DWIToDTIEstimation --enumeration LS /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLDiffusionTensorVolumeNodeC.nrrd /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLScalarVolumeNodeD.nrrd
[ERROR][VTK] 09.12.2016 08:06:16 [vtkNRRDWriter (0x10aeee860)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Base/QTCLI/vtkSlicerCLIModuleLogic.cxx, line 2147
vtkSlicerCLIModuleLogic (0x12045ce90): Diffusion Tensor Estimation standard error:

ERROR: In /Users/kitware/Dashboards/Nightly/S-0-E-b/SlicerDMRI/Libs/vtkDMRI/vtkTeemEstimateDiffusionTensor.cxx, line 272
vtkTeemEstimateDiffusionTensor (0x10aee1aa0): The input has to have a number of components equal to the number of gradients

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkExecutive.cxx, line 784
vtkCompositeDataPipeline (0x10aee31c0): Algorithm vtkTeemEstimateDiffusionTensor(0x10aee1aa0) returned failure for request: vtkInformation (0x10aee8d40)
Debug: Off
Modified Time: 563
Reference Count: 1
Registered Events: (none)
Request: REQUEST_DATA
FORWARD_DIRECTION: 0
FROM_OUTPUT_PORT: 0
ALGORITHM_AFTER_FORWARD: 1

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0/Libs/vtkTeem/vtkNRRDWriter.cxx, line 243
vtkNRRDWriter (0x10aeea800): Write: Error wrapping nrrd for /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLDiffusionTensorVolumeNodeC.nrrd:
[nrrd] nrrdWrap_nva:
[nrrd] _nrrdSizeCheck: axis 0 size is zero!

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0/Libs/vtkTeem/vtkNRRDWriter.cxx:243) - Write: Error wrapping nrrd for /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLScalarVolumeNodeD.nrrd:
[nrrd] nrrdWrap_nva:
[nrrd] _nrrdSizeCheck: axis 0 size is zero!
[DEBUG][Qt] 09.12.2016 08:06:16 [] (unknown:0) - Diffusion Tensor Estimation completed without errors
[ERROR][VTK] 09.12.2016 08:06:16 [vtkCompositeDataPipeline (0x12d673050)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12d692950) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:16 [vtkCompositeDataPipeline (0x12cfe2a50)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageThreshold(0x12cfe0b10) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:16 [vtkCompositeDataPipeline (0x12d673050)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12d692950) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:16 [vtkCompositeDataPipeline (0x12d673050)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12d692950) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:16 [vtkCompositeDataPipeline (0x12cfe2a50)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageThreshold(0x12cfe0b10) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:16 [vtkCompositeDataPipeline (0x12d673050)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12d692950) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:21 [vtkCompositeDataPipeline (0x12d673050)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12d692950) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:21 [vtkCompositeDataPipeline (0x12cfe2a50)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageThreshold(0x12cfe0b10) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:21 [vtkCompositeDataPipeline (0x12d673050)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12d692950) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:21 [vtkCompositeDataPipeline (0x12d673050)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12d692950) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:21 [vtkCompositeDataPipeline (0x12cfe2a50)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageThreshold(0x12cfe0b10) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:21 [vtkCompositeDataPipeline (0x12d673050)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkImageMapToWindowLevelColors(0x12d692950) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:22 [vtkCompositeDataPipeline (0x12cfee6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12cfed1c0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:22 [vtkCompositeDataPipeline (0x13cfcbd60)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12d68d490) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:22 [vtkCompositeDataPipeline (0x12cfee6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12cfed1c0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:22 [vtkCompositeDataPipeline (0x13cfcbd60)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12d68d490) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:34 [vtkCompositeDataPipeline (0x13cf5a070)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf587f0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:34 [vtkCompositeDataPipeline (0x13cf3c250)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf59490) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:34 [vtkCompositeDataPipeline (0x13cf5a070)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf587f0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:34 [vtkCompositeDataPipeline (0x13cf3c250)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf59490) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:39 [vtkCompositeDataPipeline (0x13cf5a070)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf587f0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:39 [vtkCompositeDataPipeline (0x13cf3c250)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf59490) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:39 [vtkCompositeDataPipeline (0x13cf5a070)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf587f0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:06:39 [vtkCompositeDataPipeline (0x13cf3c250)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf59490) has 0 connections but is not optional.
[DEBUG][Qt] 09.12.2016 08:06:46 [] (unknown:0) - Switch to module: "DiffusionWeightedVolumeMasking"
[ERROR][VTK] 09.12.2016 08:07:07 [vtkCompositeDataPipeline (0x13cf5a070)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf587f0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:07 [vtkCompositeDataPipeline (0x13cf3c250)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf59490) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:07 [vtkCompositeDataPipeline (0x13cf5a070)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf587f0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:07 [vtkCompositeDataPipeline (0x13cf3c250)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf59490) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:07 [vtkCompositeDataPipeline (0x13cf5a070)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf587f0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:07 [vtkCompositeDataPipeline (0x13cf3c250)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf59490) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:07 [vtkCompositeDataPipeline (0x13cf5a070)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf587f0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:07 [vtkCompositeDataPipeline (0x13cf3c250)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf59490) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:11 [vtkCompositeDataPipeline (0x13cf5a070)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf587f0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:11 [vtkCompositeDataPipeline (0x13cf3c250)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf59490) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:11 [vtkCompositeDataPipeline (0x13cf5a070)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf587f0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:11 [vtkCompositeDataPipeline (0x13cf3c250)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13cf59490) has 0 connections but is not optional.
[CRITICAL][FD] 09.12.2016 08:07:11 [] (unknown:0) - 2016-12-09 08:07:11.318 Slicer[30546:2021700] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[DEBUG][Qt] 09.12.2016 08:07:13 [] (unknown:0) - Found CommandLine Module, target is /Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/cli-modules/DiffusionWeightedVolumeMasking
[DEBUG][Qt] 09.12.2016 08:07:13 [] (unknown:0) - ModuleType: CommandLineModule
[DEBUG][Qt] 09.12.2016 08:07:13 [] (unknown:0) - Diffusion Brain Masking command line:

/Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/cli-modules/DiffusionWeightedVolumeMasking --baselineBValueThreshold 100 --removeislands /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLScalarVolumeNodeD.nrrd /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLLabelMapVolumeNodeB.nrrd
[DEBUG][Qt] 09.12.2016 08:07:14 [] (unknown:0) - Diffusion Brain Masking completed without errors
[INFO][VTK] 09.12.2016 08:07:15 [vtkMRMLVolumeArchetypeStorageNode (0x12e0bb980)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:456) - Loaded volume from file: /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLLabelMapVolumeNodeB.nrrd. Dimensions: 256x256x44. Number of components: 1. Pixel type: unsigned char.
[INFO][VTK] 09.12.2016 08:07:15 [vtkMRMLVolumeArchetypeStorageNode (0x12e0d1480)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:456) - Loaded volume from file: /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLScalarVolumeNodeD.nrrd. Dimensions: 256x256x44. Number of components: 1. Pixel type: short.
[INFO][Stream] 09.12.2016 08:07:15 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[DEBUG][Qt] 09.12.2016 08:07:29 [] (unknown:0) - Switch to module: "DWIToDTIEstimation"
[DEBUG][Qt] 09.12.2016 08:07:33 [] (unknown:0) - Found CommandLine Module, target is /Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/cli-modules/DWIToDTIEstimation
[DEBUG][Qt] 09.12.2016 08:07:33 [] (unknown:0) - ModuleType: CommandLineModule
[DEBUG][Qt] 09.12.2016 08:07:33 [] (unknown:0) - Diffusion Tensor Estimation command line:

/Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/cli-modules/DWIToDTIEstimation --mask /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLLabelMapVolumeNodeB.nrrd --enumeration LS /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLDiffusionTensorVolumeNodeC.nrrd /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLScalarVolumeNodeD.nrrd
[ERROR][VTK] 09.12.2016 08:07:34 [vtkNRRDWriter (0x10ad1d2c0)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Base/QTCLI/vtkSlicerCLIModuleLogic.cxx, line 2147
vtkSlicerCLIModuleLogic (0x12045ce90): Diffusion Tensor Estimation standard error:

ERROR: In /Users/kitware/Dashboards/Nightly/S-0-E-b/SlicerDMRI/Libs/vtkDMRI/vtkTeemEstimateDiffusionTensor.cxx, line 272
vtkTeemEstimateDiffusionTensor (0x10ad0d870): The input has to have a number of components equal to the number of gradients

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkExecutive.cxx, line 784
vtkCompositeDataPipeline (0x10ad0efc0): Algorithm vtkTeemEstimateDiffusionTensor(0x10ad0d870) returned failure for request: vtkInformation (0x10ad14ba0)
Debug: Off
Modified Time: 563
Reference Count: 1
Registered Events: (none)
Request: REQUEST_DATA
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0
FROM_OUTPUT_PORT: 0

ERROR: In /Users/kitware/Dashboards/Nightly/S-0-E-b/SlicerDMRI/Libs/vtkDMRI/vtkTeemEstimateDiffusionTensor.cxx, line 272
vtkTeemEstimateDiffusionTensor (0x10ad0d870): The input has to have a number of components equal to the number of gradients

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkExecutive.cxx, line 784
vtkCompositeDataPipeline (0x10ad0efc0): Algorithm vtkTeemEstimateDiffusionTensor(0x10ad0d870) returned failure for request: vtkInformation (0x10ad18dc0)
Debug: Off
Modified Time: 1332
Reference Count: 1
Registered Events: (none)
Request: REQUEST_DATA
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0
FROM_OUTPUT_PORT: 0

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0/Libs/vtkTeem/vtkNRRDWriter.cxx, line 243
vtkNRRDWriter (0x10ad19170): Write: Error wrapping nrrd for /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLDiffusionTensorVolumeNodeC.nrrd:
[nrrd] nrrdWrap_nva:
[nrrd] _nrrdSizeCheck: axis 1 size is zero!

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0/Libs/vtkTeem/vtkNRRDWriter.cxx:243) - Write: Error wrapping nrrd for /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLScalarVolumeNodeD.nrrd:
[nrrd] nrrdWrap_nva:
[nrrd] _nrrdSizeCheck: axis 1 size is zero!
[DEBUG][Qt] 09.12.2016 08:07:34 [] (unknown:0) - Diffusion Tensor Estimation completed without errors
[INFO][Stream] 09.12.2016 08:07:34 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:07:34 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[ERROR][VTK] 09.12.2016 08:07:38 [vtkCompositeDataPipeline (0x154adb690)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12cf64410) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:38 [vtkCompositeDataPipeline (0x154fe7ba0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12d6370a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:38 [vtkCompositeDataPipeline (0x154adb690)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12cf64410) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:38 [vtkCompositeDataPipeline (0x154fe7ba0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12d6370a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:42 [vtkCompositeDataPipeline (0x154adb690)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12cf64410) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:42 [vtkCompositeDataPipeline (0x154fe7ba0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12d6370a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:42 [vtkCompositeDataPipeline (0x154adb690)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12cf64410) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:07:42 [vtkCompositeDataPipeline (0x154fe7ba0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12d6370a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:30 [vtkCompositeDataPipeline (0x154adb690)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12cf64410) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:30 [vtkCompositeDataPipeline (0x154fe7ba0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12d6370a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:30 [vtkCompositeDataPipeline (0x154adb690)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12cf64410) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:30 [vtkCompositeDataPipeline (0x154fe7ba0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12d6370a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:33 [vtkCompositeDataPipeline (0x154adb690)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12cf64410) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:33 [vtkCompositeDataPipeline (0x154fe7ba0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12d6370a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:33 [vtkCompositeDataPipeline (0x154adb690)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12cf64410) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:33 [vtkCompositeDataPipeline (0x154fe7ba0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12d6370a0) has 0 connections but is not optional.
[CRITICAL][FD] 09.12.2016 08:08:33 [] (unknown:0) - 2016-12-09 08:08:33.854 Slicer[30546:2021700] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[ERROR][VTK] 09.12.2016 08:08:33 [vtkCompositeDataPipeline (0x154adb690)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12cf64410) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:33 [vtkCompositeDataPipeline (0x154fe7ba0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12d6370a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:33 [vtkCompositeDataPipeline (0x154adb690)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12cf64410) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:33 [vtkCompositeDataPipeline (0x154fe7ba0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12d6370a0) has 0 connections but is not optional.
[DEBUG][Qt] 09.12.2016 08:08:36 [] (unknown:0) - Found CommandLine Module, target is /Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/cli-modules/DWIToDTIEstimation
[DEBUG][Qt] 09.12.2016 08:08:36 [] (unknown:0) - ModuleType: CommandLineModule
[DEBUG][Qt] 09.12.2016 08:08:36 [] (unknown:0) - Diffusion Tensor Estimation command line:

/Users/johnsonhj/Desktop/Slicer.app/Contents/Extensions-25603/SlicerDMRI/lib/Slicer-4.7/cli-modules/DWIToDTIEstimation --mask /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLLabelMapVolumeNodeB.nrrd --enumeration LS /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLDiffusionTensorVolumeNodeC.nrrd /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLScalarVolumeNodeD.nrrd
[ERROR][VTK] 09.12.2016 08:08:36 [vtkNRRDWriter (0x10aed1190)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Base/QTCLI/vtkSlicerCLIModuleLogic.cxx, line 2147
vtkSlicerCLIModuleLogic (0x12045ce90): Diffusion Tensor Estimation standard error:

ERROR: In /Users/kitware/Dashboards/Nightly/S-0-E-b/SlicerDMRI/Libs/vtkDMRI/vtkTeemEstimateDiffusionTensor.cxx, line 272
vtkTeemEstimateDiffusionTensor (0x10d11bee0): The input has to have a number of components equal to the number of gradients

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkExecutive.cxx, line 784
vtkCompositeDataPipeline (0x10d11cda0): Algorithm vtkTeemEstimateDiffusionTensor(0x10d11bee0) returned failure for request: vtkInformation (0x10d1276e0)
Debug: Off
Modified Time: 563
Reference Count: 1
Registered Events: (none)
Request: REQUEST_DATA
FORWARD_DIRECTION: 0
FROM_OUTPUT_PORT: 0
ALGORITHM_AFTER_FORWARD: 1

ERROR: In /Users/kitware/Dashboards/Nightly/S-0-E-b/SlicerDMRI/Libs/vtkDMRI/vtkTeemEstimateDiffusionTensor.cxx, line 272
vtkTeemEstimateDiffusionTensor (0x10d11bee0): The input has to have a number of components equal to the number of gradients

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkExecutive.cxx, line 784
vtkCompositeDataPipeline (0x10d11cda0): Algorithm vtkTeemEstimateDiffusionTensor(0x10d11bee0) returned failure for request: vtkInformation (0x10aecca50)
Debug: Off
Modified Time: 1332
Reference Count: 1
Registered Events: (none)
Request: REQUEST_DATA
FORWARD_DIRECTION: 0
FROM_OUTPUT_PORT: 0
ALGORITHM_AFTER_FORWARD: 1

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0/Libs/vtkTeem/vtkNRRDWriter.cxx, line 243
vtkNRRDWriter (0x10aecd040): Write: Error wrapping nrrd for /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLDiffusionTensorVolumeNodeC.nrrd:
[nrrd] nrrdWrap_nva:
[nrrd] _nrrdSizeCheck: axis 1 size is zero!

ERROR: In /Users/kitware/Dashboards/Nightly/Slicer-0/Libs/vtkTeem/vtkNRRDWriter.cxx:243) - Write: Error wrapping nrrd for /Users/johnsonhj/Slicer/data/DAFEG_vtkMRMLScalarVolumeNodeD.nrrd:
[nrrd] nrrdWrap_nva:
[nrrd] _nrrdSizeCheck: axis 1 size is zero!
[DEBUG][Qt] 09.12.2016 08:08:36 [] (unknown:0) - Diffusion Tensor Estimation completed without errors
[INFO][Stream] 09.12.2016 08:08:37 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:08:37 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[ERROR][VTK] 09.12.2016 08:08:41 [vtkCompositeDataPipeline (0x13ef5f6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13ef1d6a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:41 [vtkCompositeDataPipeline (0x13cf54ea0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0c57a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:41 [vtkCompositeDataPipeline (0x13ef5f6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13ef1d6a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:08:41 [vtkCompositeDataPipeline (0x13cf54ea0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0c57a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:09:02 [vtkCompositeDataPipeline (0x13ef5f6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13ef1d6a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:09:02 [vtkCompositeDataPipeline (0x13cf54ea0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0c57a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:09:02 [vtkCompositeDataPipeline (0x13ef5f6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13ef1d6a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:09:02 [vtkCompositeDataPipeline (0x13cf54ea0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0c57a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:09:07 [vtkCompositeDataPipeline (0x13ef5f6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13ef1d6a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:09:07 [vtkCompositeDataPipeline (0x13cf54ea0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0c57a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:09:07 [vtkCompositeDataPipeline (0x13ef5f6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13ef1d6a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:09:07 [vtkCompositeDataPipeline (0x13cf54ea0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0c57a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:12:37 [vtkCompositeDataPipeline (0x13ef5f6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13ef1d6a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:12:37 [vtkCompositeDataPipeline (0x13cf54ea0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0c57a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:12:37 [vtkCompositeDataPipeline (0x13ef5f6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13ef1d6a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:12:37 [vtkCompositeDataPipeline (0x13cf54ea0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0c57a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:12:41 [vtkCompositeDataPipeline (0x13ef5f6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13ef1d6a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:12:41 [vtkCompositeDataPipeline (0x13cf54ea0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0c57a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:12:41 [vtkCompositeDataPipeline (0x13ef5f6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13ef1d6a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:12:41 [vtkCompositeDataPipeline (0x13cf54ea0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0c57a0) has 0 connections but is not optional.
[CRITICAL][FD] 09.12.2016 08:12:55 [] (unknown:0) - 2016-12-09 08:12:55.894 Slicer[30546:2021700] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[ERROR][VTK] 09.12.2016 08:12:57 [vtkCompositeDataPipeline (0x13ef5f6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13ef1d6a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:12:57 [vtkCompositeDataPipeline (0x13cf54ea0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0c57a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:12:57 [vtkCompositeDataPipeline (0x13ef5f6a0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x13ef1d6a0) has 0 connections but is not optional.
[ERROR][VTK] 09.12.2016 08:12:57 [vtkCompositeDataPipeline (0x13cf54ea0)] (/Users/kitware/Dashboards/Nightly/Slicer-0-build/VTKv7/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx:710) - Input port 0 of algorithm vtkDiffusionTensorMathematics(0x12e0c57a0) has 0 connections but is not optional.
[CRITICAL][FD] 09.12.2016 08:12:57 [] (unknown:0) - 2016-12-09 08:12:57.079 Slicer[30546:2021700] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[INFO][VTK] 09.12.2016 08:12:58 [vtkMRMLVolumeArchetypeStorageNode (0x140436070)] (/Users/kitware/Dashboards/Nightly/Slicer-0/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:456) - Loaded volume from file: /Users/johnsonhj/src/BT-11/BRAINSTools-build/DWIConvert/test99/GeSignaHDx/SlicerTest_DTI.nrrd. Dimensions: 256x256x44. Number of components: 1. Pixel type: double.
[INFO][Stream] 09.12.2016 08:12:58 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:12:58 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:12:58 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:12:58 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[DEBUG][Qt] 09.12.2016 08:12:58 [] (unknown:0) - "Volume" Reader has successfully read the file "/Users/johnsonhj/src/BT-11/BRAINSTools-build/DWIConvert/test99/GeSignaHDx/SlicerTest_DTI.nrrd" "[1.24s]"
[DEBUG][Qt] 09.12.2016 08:13:30 [] (unknown:0) - Switch to module: "Volumes"
[WARNING][Qt] 09.12.2016 08:13:31 [] (unknown:0) - ctkDoubleRangeSlider::setSingleStep( 100 ) is outside of valid bounds.
[WARNING][Qt] 09.12.2016 08:13:31 [] (unknown:0) - ctkRangeWidget::setSingleStep( 100 ) is outside valid bounds
[WARNING][Qt] 09.12.2016 08:13:32 [] (unknown:0) - QPixmap::scaled: Pixmap is a null pixmap
[WARNING][Qt] 09.12.2016 08:13:33 [] (unknown:0) - no dataArray
[INFO][Stream] 09.12.2016 08:13:36 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[WARNING][Qt] 09.12.2016 08:13:37 [] (unknown:0) - QPixmap::scaled: Pixmap is a null pixmap
[INFO][Stream] 09.12.2016 08:13:38 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:38 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[WARNING][Qt] 09.12.2016 08:13:39 [] (unknown:0) - QPixmap::scaled: Pixmap is a null pixmap
[INFO][Stream] 09.12.2016 08:13:40 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:46 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:46 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:46 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:46 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:46 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:47 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:47 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:47 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:47 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:47 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:47 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:47 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:47 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:47 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:47 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayableManager::vtkInternal::UpdateVolumeDisplayNode()
[INFO][Stream] 09.12.2016 08:13:47 [] (unknown:0) - vtkMRMLVolumeGlyphSliceDisplayab

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Activities

inorton

inorton

2016-12-09 12:25

developer   ~0014271

I'm having trouble reproducing this in 4.6.2, yesterday's nightly, or a fully updated local trunk build. Tested both the "DWIVolume" sample dataset and the GeSignaHDx BRAINSTools test dataset [1].

For the latter I did:

  • run DWIConvert on the DICOM dir
  • save resulting nrrd from Slicer
  • quit and restart Slicer
  • reload DWI nrrd
  • run tensor estimation -- it completes successfully.

[1] http://slicer.kitware.com/midas3/item/92995
inorton

inorton

2016-12-09 12:26

developer   ~0014272

Could you try setting "Prefer executable CLI" to "yes"? I tried both ways and it works, but maybe there is some further issue on OSX 10.12. I'm still on 10.11.
inorton

inorton

2017-06-09 10:30

developer   ~0014685

Please comment/reopen if this is still an issue.

Issue History

Date Modified Username Field Change
2016-12-09 09:36 hjmjohnson New Issue
2016-12-09 09:36 hjmjohnson Status new => assigned
2016-12-09 09:36 hjmjohnson Assigned To => inorton
2016-12-09 12:25 inorton Note Added: 0014271
2016-12-09 12:26 inorton Note Added: 0014272
2017-06-09 10:30 inorton Status assigned => closed
2017-06-09 10:30 inorton Resolution open => fixed
2017-06-09 10:30 inorton Note Added: 0014685