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logger
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find . -name "*.py" | xargs perl -pi -e 's/[ \t]*$//'
Reverting test_docparse
git checkout nipype/utils/tests/test_docparse.py
building docs
make -C doc clean html
rm -rf _build/* *~ api/generated interfaces/generated users/examples documentation.zip
mkdir -p users/examples
../tools/make_examples.py --no-exec
examples2rst finished.
rm -rf api/generated
python ../tools/build_modref_templates.py
('WARNING: Empty -', 'nipype.caching')
('WARNING: Empty -', 'nipype.interfaces')
('WARNING: Empty -', 'nipype.pipeline')
4 files written
rm -rf interfaces/generated
python ../tools/build_interface_docs.py
121117-19:30:49,17 workflow DEBUG:
networkx 1.4 dev or higher detected
Installed version: 0.7.0.gb101a53-dev
Current stable version: 0.6.0
Current dev version: 0.7.0.g47cdfdb-dev
WARNING: Empty - nipype
WARNING: Empty - nipype.algorithms
ICC
AddCSVColumn
CreateNifti
Distance
Gunzip
Matlab2CSV
MergeCSVFiles
ModifyAffine
Overlap
PickAtlas
SimpleThreshold
TSNR
SpecifyModel
SpecifySPMModel
SpecifySparseModel
SpecifySparseSPMModel
'SpecifySparseSPMModel'
ArtifactDetect
StimulusCorrelation
WARNING: Empty - nipype.info
WARNING: Empty - nipype.interfaces
WARNING: Empty - nipype.interfaces.afni
WARNING: Empty - nipype.interfaces.afni.base
Allineate
Automask
BrickStat
Calc
Copy
Despike
Detrend
Fim
Fourier
Maskave
Merge
ROIStats
Refit
Resample
SkullStrip
TCat
TCorrelate
TShift
TStat
To3D
Volreg
Warp
ZCutUp
WARNING: Empty - nipype.interfaces.ants
WARNING: Empty - nipype.interfaces.ants.base
GenWarpFields
antsIntroduction
buildtemplateparallel
Registration
ApplyTransforms
WarpImageMultiTransform
WarpTimeSeriesImageMultiTransform
Atropos
N4BiasFieldCorrection
AverageAffineTransform
AverageImages
MultiplyImages
WARNING: Empty - nipype.interfaces.camino
Conmap
AnalyzeHeader
DT2NIfTI
Image2Voxel
NIfTIDT2Camino
ProcStreamlines
TractShredder
VtkStreamlines
ComputeEigensystem
ComputeFractionalAnisotropy
ComputeMeanDiffusivity
ComputeTensorTrace
DTIFit
DTLUTGen
ModelFit
PicoPDFs
Track
TrackBallStick
TrackBayesDirac
TrackBootstrap
TrackDT
TrackPICo
WARNING: Empty - nipype.interfaces.camino2trackvis
Camino2Trackvis
Trackvis2Camino
WARNING: Empty - nipype.interfaces.cmtk
CreateMatrix
CreateNodes
ROIGen
CFFConverter
MergeCNetworks
NetworkBasedStatistic
AverageNetworks
NetworkXMetrics
Parcellate
Dcm2nii
WARNING: Empty - nipype.interfaces.diffusion_toolkit
WARNING: Empty - nipype.interfaces.diffusion_toolkit.base
DTIRecon
DTITracker
HARDIMat
ODFRecon
ODFTracker
SplineFilter
WARNING: Empty - nipype.interfaces.dipy
TrackDensityMap
SlicerCommandLine
WARNING: Empty - nipype.interfaces.freesurfer
WARNING: Empty - nipype.interfaces.freesurfer.base
Binarize
Concatenate
GLMFit
Label2Vol
MRISPreproc
MS_LDA
OneSampleTTest
SegStats
ApplyVolTransform
BBRegister
DICOMConvert
FitMSParams
MRIConvert
ParseDICOMDir
ReconAll
Resample
RobustRegister
Smooth
SynthesizeFLASH
UnpackSDICOMDir
ApplyMask
MRIMarchingCubes
MRITessellate
MRIsConvert
MakeAverageSubject
SampleToSurface
SmoothTessellation
SurfaceSmooth
SurfaceSnapshots
SurfaceTransform
WARNING: Empty - nipype.interfaces.fsl
WARNING: Empty - nipype.interfaces.fsl.base
BEDPOSTX
DTIFit
DistanceMap
EddyCorrect
FindTheBiggest
MakeDyadicVectors
ProbTrackX
ProjThresh
TractSkeleton
VecReg
XFibres
ApplyMask
ApplyMaskInput
BinaryMaths
BinaryMathsInput
ChangeDataType
ChangeDataTypeInput
DilateImage
DilateInput
ErodeImage
ErodeInput
IsotropicSmooth
IsotropicSmoothInput
KernelInput
MathsCommand
MathsInput
MathsOutput
MeanImage
MeanImageInput
MultiImageMaths
MultiImageMathsInput
SpatialFilter
SpatialFilterInput
TemporalFilter
TemporalFilterInput
Threshold
UnaryMaths
UnaryMathsInput
Cluster
ContrastMgr
FEAT
FEATModel
FEATRegister
FILMGLS
FLAMEO
L2Model
Level1Design
MELODIC
MultipleRegressDesign
Randomise
SMM
SmoothEstimate
ApplyWarp
ApplyXfm
BET
FAST
FIRST
FLIRT
FNIRT
FUGUE
MCFLIRT
PRELUDE
SUSAN
SliceTimer
AvScale
ConvertXFM
EPIDeWarp
ExtractROI
FilterRegressor
ImageMaths
ImageMeants
ImageStats
Merge
Overlay
PlotMotionParams
PlotTimeSeries
PowerSpectrum
Reorient2Std
Slicer
Smooth
Split
SwapDimensions
DataGrabber
DataSink
FreeSurferSource
IOBase
MySQLSink
SQLiteSink
XNATSink
XNATSource
MeshFix
WARNING: Empty - nipype.interfaces.mne
WatershedBEM
WARNING: Empty - nipype.interfaces.mrtrix
MRTrix2TrackVis
DWI2Tensor
Erode
GenerateWhiteMatterMask
MRConvert
MRMultiply
MRTransform
MRTrixViewer
MedianFilter3D
Tensor2ApparentDiffusion
Tensor2FractionalAnisotropy
Tensor2Vector
Threshold
ConstrainedSphericalDeconvolution
DWI2SphericalHarmonicsImage
EstimateResponseForSH
DiffusionTensorStreamlineTrack
ProbabilisticSphericallyDeconvolutedStreamlineTrack
SphericallyDeconvolutedStreamlineTrack
StreamlineTrack
Tracks2Prob
WARNING: Empty - nipype.interfaces.nipy
EstimateContrast
FitGLM
ComputeMask
FmriRealign4d
Similarity
WARNING: Empty - nipype.interfaces.nitime
CoherenceAnalyzer
GetTimeSeries
WARNING: Empty - nipype.interfaces.slicer
SlicerCommandLine
DicomToNrrdConverter
WARNING: Empty - nipype.interfaces.slicer.diffusion
dwiNoiseFilter
jointLMMSE
extractNrrdVectorIndex
gtractAnisotropyMap
gtractAverageBvalues
gtractClipAnisotropy
gtractCoRegAnatomy
gtractConcatDwi
gtractCopyImageOrientation
gtractCoregBvalues
gtractCostFastMarching
gtractImageConformity
gtractInvertBSplineTransform
gtractInvertDeformationField
gtractInvertRigidTransform
gtractResampleAnisotropy
gtractResampleB0
gtractResampleCodeImage
gtractResampleDWIInPlace
gtractTensor
gtractTransformToDeformationField
DiffusionTensorEstimation
DiffusionTensorMathematics
DiffusionWeightedMasking
ResampleDTI
WARNING: Empty - nipype.interfaces.slicer.filtering
Add
Cast
CheckerBoard
CurvatureAnisotropicDiffusion
WARNING: Empty - nipype.interfaces.slicer.legacy
WARNING: Empty - nipype.interfaces.slicer.legacy.diffusion
dwiUNLM
AffineRegistration
BSplineDeformableRegistration
DiffusionTensorTest
ComputeSUVBodyWeight
BRAINSDemonWarp
BRAINSFit
BRAINSResample
VBRAINSDemonWarp
WARNING: Empty - nipype.interfaces.slicer.segmentation
ConfidenceConnected
BRAINSROIAuto
WARNING: Empty - nipype.interfaces.spm
EstimateContrast
EstimateModel
FactorialDesign
Level1Design
MultipleRegressionDesign
OneSampleTTestDesign
PairedTTestDesign
Threshold
ThresholdStatistics
TwoSampleTTestDesign
ApplyDeformations
Coregister
CreateWarped
DARTEL
DARTELNorm2MNI
NewSegment
Normalize
Realign
Segment
SliceTiming
Smooth
Analyze2nii
ApplyTransform
CalcCoregAffine
Reslice
AssertEqual
Function
IdentityInterface
Merge
Rename
Select
Split
WARNING: Empty - nipype.workflows
WARNING: Empty - nipype.workflows.dmri
WARNING: Empty - nipype.workflows.dmri.camino
121117-19:30:55,835 workflow DEBUG:
(mapping.inputnode_within, mapping.fssource): No edge data
121117-19:30:55,835 workflow DEBUG:
(mapping.inputnode_within, mapping.fssource): new edge data: {'connect': [('subjects_dir', 'subjects_dir')]}
121117-19:30:55,836 workflow DEBUG:
(mapping.inputnode_within, mapping.fssource): Edge data exists: {'connect': [('subjects_dir', 'subjects_dir')]}
121117-19:30:55,836 workflow DEBUG:
(mapping.inputnode_within, mapping.fssource): new edge data: {'connect': [('subjects_dir', 'subjects_dir'), ('subject_id', 'subject_id')]}
121117-19:30:55,836 workflow DEBUG:
(mapping.inputnode_within, mapping.fssourceLH): No edge data
121117-19:30:55,836 workflow DEBUG:
(mapping.inputnode_within, mapping.fssourceLH): new edge data: {'connect': [('subjects_dir', 'subjects_dir')]}
121117-19:30:55,837 workflow DEBUG:
(mapping.inputnode_within, mapping.fssourceLH): Edge data exists: {'connect': [('subjects_dir', 'subjects_dir')]}
121117-19:30:55,837 workflow DEBUG:
(mapping.inputnode_within, mapping.fssourceLH): new edge data: {'connect': [('subjects_dir', 'subjects_dir'), ('subject_id', 'subject_id')]}
121117-19:30:55,837 workflow DEBUG:
(mapping.inputnode_within, mapping.fssourceRH): No edge data
121117-19:30:55,837 workflow DEBUG:
(mapping.inputnode_within, mapping.fssourceRH): new edge data: {'connect': [('subjects_dir', 'subjects_dir')]}
121117-19:30:55,838 workflow DEBUG:
(mapping.inputnode_within, mapping.fssourceRH): Edge data exists: {'connect': [('subjects_dir', 'subjects_dir')]}
121117-19:30:55,838 workflow DEBUG:
(mapping.inputnode_within, mapping.fssourceRH): new edge data: {'connect': [('subjects_dir', 'subjects_dir'), ('subject_id', 'subject_id')]}
121117-19:30:55,840 workflow DEBUG:
(mapping.inputnode_within, mapping.image2voxel): No edge data
121117-19:30:55,840 workflow DEBUG:
(mapping.inputnode_within, mapping.image2voxel): new edge data: {'connect': [('dwi', 'in_file')]}
121117-19:30:55,840 workflow DEBUG:
(mapping.inputnode_within, mapping.fsl2scheme): No edge data
121117-19:30:55,840 workflow DEBUG:
(mapping.inputnode_within, mapping.fsl2scheme): new edge data: {'connect': [('bvecs', 'bvec_file'), ('bvals', 'bval_file')]}
121117-19:30:55,840 workflow DEBUG:
(mapping.image2voxel, mapping.dtifit): No edge data
121117-19:30:55,840 workflow DEBUG:
(mapping.image2voxel, mapping.dtifit): new edge data: {'connect': [['voxel_order', 'in_file']]}
121117-19:30:55,840 workflow DEBUG:
(mapping.fsl2scheme, mapping.dtifit): No edge data
121117-19:30:55,840 workflow DEBUG:
(mapping.fsl2scheme, mapping.dtifit): new edge data: {'connect': [['scheme', 'scheme_file']]}
121117-19:30:55,840 workflow DEBUG:
(mapping.fssource, mapping.mri_convert_Brain): No edge data
121117-19:30:55,840 workflow DEBUG:
(mapping.fssource, mapping.mri_convert_Brain): new edge data: {'connect': [('brain', 'in_file')]}
121117-19:30:55,840 workflow DEBUG:
(mapping.fssourceLH, mapping.mris_convertLH): No edge data
121117-19:30:55,841 workflow DEBUG:
(mapping.fssourceLH, mapping.mris_convertLH): new edge data: {'connect': [('pial', 'in_file')]}
121117-19:30:55,841 workflow DEBUG:
(mapping.fssourceRH, mapping.mris_convertRH): No edge data
121117-19:30:55,841 workflow DEBUG:
(mapping.fssourceRH, mapping.mris_convertRH): new edge data: {'connect': [('pial', 'in_file')]}
121117-19:30:55,841 workflow DEBUG:
(mapping.fssourceLH, mapping.mris_convertLHwhite): No edge data
121117-19:30:55,841 workflow DEBUG:
(mapping.fssourceLH, mapping.mris_convertLHwhite): new edge data: {'connect': [('white', 'in_file')]}
121117-19:30:55,841 workflow DEBUG:
(mapping.fssourceRH, mapping.mris_convertRHwhite): No edge data
121117-19:30:55,841 workflow DEBUG:
(mapping.fssourceRH, mapping.mris_convertRHwhite): new edge data: {'connect': [('white', 'in_file')]}
121117-19:30:55,841 workflow DEBUG:
(mapping.fssourceLH, mapping.mris_convertLHinflated): No edge data
121117-19:30:55,841 workflow DEBUG:
(mapping.fssourceLH, mapping.mris_convertLHinflated): new edge data: {'connect': [('inflated', 'in_file')]}
121117-19:30:55,842 workflow DEBUG:
(mapping.fssourceRH, mapping.mris_convertRHinflated): No edge data
121117-19:30:55,842 workflow DEBUG:
(mapping.fssourceRH, mapping.mris_convertRHinflated): new edge data: {'connect': [('inflated', 'in_file')]}
121117-19:30:55,842 workflow DEBUG:
(mapping.fssourceLH, mapping.mris_convertLHsphere): No edge data
121117-19:30:55,842 workflow DEBUG:
(mapping.fssourceLH, mapping.mris_convertLHsphere): new edge data: {'connect': [('sphere', 'in_file')]}
121117-19:30:55,842 workflow DEBUG:
(mapping.fssourceRH, mapping.mris_convertRHsphere): No edge data
121117-19:30:55,842 workflow DEBUG:
(mapping.fssourceRH, mapping.mris_convertRHsphere): new edge data: {'connect': [('sphere', 'in_file')]}
121117-19:30:55,842 workflow DEBUG:
(mapping.fssourceLH, mapping.mris_convertLHlabels): No edge data
121117-19:30:55,842 workflow DEBUG:
(mapping.fssourceLH, mapping.mris_convertLHlabels): new edge data: {'connect': [('pial', 'in_file')]}
121117-19:30:55,842 workflow DEBUG:
(mapping.fssourceRH, mapping.mris_convertRHlabels): No edge data
121117-19:30:55,842 workflow DEBUG:
(mapping.fssourceRH, mapping.mris_convertRHlabels): new edge data: {'connect': [('pial', 'in_file')]}
121117-19:30:55,843 workflow DEBUG:
(mapping.fssourceLH, mapping.mris_convertLHlabels): Edge data exists: {'connect': [('pial', 'in_file')]}
121117-19:30:55,843 workflow DEBUG:
(mapping.fssourceLH, mapping.mris_convertLHlabels): new edge data: {'connect': [('pial', 'in_file'), (('annot', 'S"def select_aparc_annot(list_of_files):\\n for in_file in list_of_files:\\n if \'.aparc.annot\' in in_file:\\n idx = list_of_files.index(in_file)\\n return list_of_files[idx]\\n"\n.', ()), 'annot_file')]}
121117-19:30:55,844 workflow DEBUG:
(mapping.fssourceRH, mapping.mris_convertRHlabels): Edge data exists: {'connect': [('pial', 'in_file')]}
121117-19:30:55,844 workflow DEBUG:
(mapping.fssourceRH, mapping.mris_convertRHlabels): new edge data: {'connect': [('pial', 'in_file'), (('annot', 'S"def select_aparc_annot(list_of_files):\\n for in_file in list_of_files:\\n if \'.aparc.annot\' in in_file:\\n idx = list_of_files.index(in_file)\\n return list_of_files[idx]\\n"\n.', ()), 'annot_file')]}
121117-19:30:55,844 workflow DEBUG:
(mapping.inputnode_within, mapping.bet_b0): No edge data
121117-19:30:55,845 workflow DEBUG:
(mapping.inputnode_within, mapping.bet_b0): new edge data: {'connect': [('dwi', 'in_file')]}
121117-19:30:55,845 workflow DEBUG:
(mapping.inputnode_within, mapping.bet_b0): Edge data exists: {'connect': [('dwi', 'in_file')]}
121117-19:30:55,845 workflow DEBUG:
(mapping.inputnode_within, mapping.bet_b0): new edge data: {'connect': [('dwi', 'in_file'), ('dwi', 't2_guided')]}
121117-19:30:55,846 workflow DEBUG:
(mapping.bet_b0, mapping.coregister): No edge data
121117-19:30:55,846 workflow DEBUG:
(mapping.bet_b0, mapping.coregister): new edge data: {'connect': [('out_file', 'in_file')]}
121117-19:30:55,846 workflow DEBUG:
(mapping.mri_convert_Brain, mapping.coregister): No edge data
121117-19:30:55,846 workflow DEBUG:
(mapping.mri_convert_Brain, mapping.coregister): new edge data: {'connect': [('out_file', 'reference')]}
121117-19:30:55,846 workflow DEBUG:
(mapping.coregister, mapping.convertxfm): No edge data
121117-19:30:55,846 workflow DEBUG:
(mapping.coregister, mapping.convertxfm): new edge data: {'connect': [('out_matrix_file', 'in_file')]}
121117-19:30:55,847 workflow DEBUG:
(mapping.bet_b0, mapping.inverse): No edge data
121117-19:30:55,847 workflow DEBUG:
(mapping.bet_b0, mapping.inverse): new edge data: {'connect': [('out_file', 'reference')]}
121117-19:30:55,847 workflow DEBUG:
(mapping.convertxfm, mapping.inverse): No edge data
121117-19:30:55,847 workflow DEBUG:
(mapping.convertxfm, mapping.inverse): new edge data: {'connect': [('out_file', 'in_matrix_file')]}
121117-19:30:55,847 workflow DEBUG:
(mapping.mri_convert_Brain, mapping.inverse): No edge data
121117-19:30:55,847 workflow DEBUG:
(mapping.mri_convert_Brain, mapping.inverse): new edge data: {'connect': [('out_file', 'in_file')]}
121117-19:30:55,848 workflow DEBUG:
(mapping.bet_b0, mapping.track): No edge data
121117-19:30:55,848 workflow DEBUG:
(mapping.bet_b0, mapping.track): new edge data: {'connect': [('mask_file', 'seed_file')]}
121117-19:30:55,848 workflow DEBUG:
(mapping.fsl2scheme, mapping.dtlutgen): No edge data
121117-19:30:55,848 workflow DEBUG:
(mapping.fsl2scheme, mapping.dtlutgen): new edge data: {'connect': [('scheme', 'scheme_file')]}
121117-19:30:55,848 workflow DEBUG:
(mapping.dtlutgen, mapping.picopdfs): No edge data
121117-19:30:55,848 workflow DEBUG:
(mapping.dtlutgen, mapping.picopdfs): new edge data: {'connect': [('dtLUT', 'luts')]}
121117-19:30:55,848 workflow DEBUG:
(mapping.dtifit, mapping.picopdfs): No edge data
121117-19:30:55,849 workflow DEBUG:
(mapping.dtifit, mapping.picopdfs): new edge data: {'connect': [('tensor_fitted', 'in_file')]}
121117-19:30:55,849 workflow DEBUG:
(mapping.picopdfs, mapping.track): No edge data
121117-19:30:55,849 workflow DEBUG:
(mapping.picopdfs, mapping.track): new edge data: {'connect': [('pdfs', 'in_file')]}
121117-19:30:55,849 workflow DEBUG:
(mapping.dtifit, mapping.fa): No edge data
121117-19:30:55,849 workflow DEBUG:
(mapping.dtifit, mapping.fa): new edge data: {'connect': [('tensor_fitted', 'in_file')]}
121117-19:30:55,849 workflow DEBUG:
(mapping.fa, mapping.analyzeheader_fa): No edge data
121117-19:30:55,849 workflow DEBUG:
(mapping.fa, mapping.analyzeheader_fa): new edge data: {'connect': [('fa', 'in_file')]}
121117-19:30:55,852 workflow DEBUG:
(mapping.inputnode_within, mapping.analyzeheader_fa): No edge data
121117-19:30:55,852 workflow DEBUG:
(mapping.inputnode_within, mapping.analyzeheader_fa): new edge data: {'connect': [(('dwi', "S'def get_vox_dims(volume):\\n import nibabel as nb\\n if isinstance(volume, list):\\n volume = volume[0]\\n nii = nb.load(volume)\\n hdr = nii.get_header()\\n voxdims = hdr.get_zooms()\\n return [float(voxdims[0]), float(voxdims[1]), float(voxdims[2])]\\n'\n.", ()), 'voxel_dims'), (('dwi', "S'def get_data_dims(volume):\\n import nibabel as nb\\n if isinstance(volume, list):\\n volume = volume[0]\\n nii = nb.load(volume)\\n hdr = nii.get_header()\\n datadims = hdr.get_data_shape()\\n return [int(datadims[0]), int(datadims[1]), int(datadims[2])]\\n'\n.", ()), 'data_dims')]}
121117-19:30:55,852 workflow DEBUG:
(mapping.fa, mapping.fa2nii): No edge data
121117-19:30:55,852 workflow DEBUG:
(mapping.fa, mapping.fa2nii): new edge data: {'connect': [('fa', 'data_file')]}
121117-19:30:55,853 workflow DEBUG:
(mapping.inputnode_within, mapping.fa2nii): No edge data
121117-19:30:55,853 workflow DEBUG:
(mapping.inputnode_within, mapping.fa2nii): new edge data: {'connect': [(('dwi', "S'def get_affine(volume):\\n import nibabel as nb\\n nii = nb.load(volume)\\n return nii.get_affine()\\n'\n.", ()), 'affine')]}
121117-19:30:55,853 workflow DEBUG:
(mapping.analyzeheader_fa, mapping.fa2nii): No edge data
121117-19:30:55,854 workflow DEBUG:
(mapping.analyzeheader_fa, mapping.fa2nii): new edge data: {'connect': [('header', 'header_file')]}
121117-19:30:55,854 workflow DEBUG:
(mapping.dtifit, mapping.trace): No edge data
121117-19:30:55,854 workflow DEBUG:
(mapping.dtifit, mapping.trace): new edge data: {'connect': [('tensor_fitted', 'in_file')]}
121117-19:30:55,854 workflow DEBUG:
(mapping.trace, mapping.analyzeheader_trace): No edge data
121117-19:30:55,854 workflow DEBUG:
(mapping.trace, mapping.analyzeheader_trace): new edge data: {'connect': [('trace', 'in_file')]}
121117-19:30:55,857 workflow DEBUG:
(mapping.inputnode_within, mapping.analyzeheader_trace): No edge data
121117-19:30:55,857 workflow DEBUG:
(mapping.inputnode_within, mapping.analyzeheader_trace): new edge data: {'connect': [(('dwi', "S'def get_vox_dims(volume):\\n import nibabel as nb\\n if isinstance(volume, list):\\n volume = volume[0]\\n nii = nb.load(volume)\\n hdr = nii.get_header()\\n voxdims = hdr.get_zooms()\\n return [float(voxdims[0]), float(voxdims[1]), float(voxdims[2])]\\n'\n.", ()), 'voxel_dims'), (('dwi', "S'def get_data_dims(volume):\\n import nibabel as nb\\n if isinstance(volume, list):\\n volume = volume[0]\\n nii = nb.load(volume)\\n hdr = nii.get_header()\\n datadims = hdr.get_data_shape()\\n return [int(datadims[0]), int(datadims[1]), int(datadims[2])]\\n'\n.", ()), 'data_dims')]}
121117-19:30:55,857 workflow DEBUG:
(mapping.trace, mapping.trace2nii): No edge data
121117-19:30:55,857 workflow DEBUG:
(mapping.trace, mapping.trace2nii): new edge data: {'connect': [('trace', 'data_file')]}
121117-19:30:55,858 workflow DEBUG:
(mapping.inputnode_within, mapping.trace2nii): No edge data
121117-19:30:55,858 workflow DEBUG:
(mapping.inputnode_within, mapping.trace2nii): new edge data: {'connect': [(('dwi', "S'def get_affine(volume):\\n import nibabel as nb\\n nii = nb.load(volume)\\n return nii.get_affine()\\n'\n.", ()), 'affine')]}
121117-19:30:55,858 workflow DEBUG:
(mapping.analyzeheader_trace, mapping.trace2nii): No edge data
121117-19:30:55,858 workflow DEBUG:
(mapping.analyzeheader_trace, mapping.trace2nii): new edge data: {'connect': [('header', 'header_file')]}
121117-19:30:55,858 workflow DEBUG:
(mapping.dtifit, mapping.dteig): No edge data
121117-19:30:55,858 workflow DEBUG:
(mapping.dtifit, mapping.dteig): new edge data: {'connect': [('tensor_fitted', 'in_file')]}
121117-19:30:55,859 workflow DEBUG:
(mapping.track, mapping.camino2trackvis): No edge data
121117-19:30:55,859 workflow DEBUG:
(mapping.track, mapping.camino2trackvis): new edge data: {'connect': [('tracked', 'in_file')]}
121117-19:30:55,859 workflow DEBUG:
(mapping.track, mapping.vtkstreamlines): No edge data
121117-19:30:55,859 workflow DEBUG:
(mapping.track, mapping.vtkstreamlines): new edge data: {'connect': [['tracked', 'in_file']]}
121117-19:30:55,859 workflow DEBUG:
(mapping.camino2trackvis, mapping.trk2camino): No edge data
121117-19:30:55,859 workflow DEBUG:
(mapping.camino2trackvis, mapping.trk2camino): new edge data: {'connect': [['trackvis', 'in_file']]}
121117-19:30:55,862 workflow DEBUG:
(mapping.inputnode_within, mapping.camino2trackvis): No edge data
121117-19:30:55,862 workflow DEBUG:
(mapping.inputnode_within, mapping.camino2trackvis): new edge data: {'connect': [(('dwi', "S'def get_vox_dims(volume):\\n import nibabel as nb\\n if isinstance(volume, list):\\n volume = volume[0]\\n nii = nb.load(volume)\\n hdr = nii.get_header()\\n voxdims = hdr.get_zooms()\\n return [float(voxdims[0]), float(voxdims[1]), float(voxdims[2])]\\n'\n.", ()), 'voxel_dims'), (('dwi', "S'def get_data_dims(volume):\\n import nibabel as nb\\n if isinstance(volume, list):\\n volume = volume[0]\\n nii = nb.load(volume)\\n hdr = nii.get_header()\\n datadims = hdr.get_data_shape()\\n return [int(datadims[0]), int(datadims[1]), int(datadims[2])]\\n'\n.", ()), 'data_dims')]}
121117-19:30:55,862 workflow DEBUG:
(mapping.inputnode_within, mapping.CreateNodes): No edge data
121117-19:30:55,862 workflow DEBUG:
(mapping.inputnode_within, mapping.CreateNodes): new edge data: {'connect': [('resolution_network_file', 'resolution_network_file')]}
121117-19:30:55,863 workflow DEBUG:
(mapping.CreateNodes, mapping.CreateMatrix): No edge data
121117-19:30:55,863 workflow DEBUG:
(mapping.CreateNodes, mapping.CreateMatrix): new edge data: {'connect': [('node_network', 'resolution_network_file')]}
121117-19:30:55,863 workflow DEBUG:
(mapping.fssource, mapping.mri_convert_AparcAseg): No edge data
121117-19:30:55,863 workflow DEBUG:
(mapping.fssource, mapping.mri_convert_AparcAseg): new edge data: {'connect': [(('aparc_aseg', 'S"def select_aparc(list_of_files):\\n for in_file in list_of_files:\\n if \'aparc+aseg.mgz\' in in_file:\\n idx = list_of_files.index(in_file)\\n return list_of_files[idx]\\n"\n.', ()), 'in_file')]}
121117-19:30:55,864 workflow DEBUG:
(mapping.bet_b0, mapping.inverse_AparcAseg): No edge data
121117-19:30:55,864 workflow DEBUG:
(mapping.bet_b0, mapping.inverse_AparcAseg): new edge data: {'connect': [('out_file', 'reference')]}
121117-19:30:55,864 workflow DEBUG:
(mapping.convertxfm, mapping.inverse_AparcAseg): No edge data
121117-19:30:55,864 workflow DEBUG:
(mapping.convertxfm, mapping.inverse_AparcAseg): new edge data: {'connect': [('out_file', 'in_matrix_file')]}
121117-19:30:55,864 workflow DEBUG:
(mapping.mri_convert_AparcAseg, mapping.inverse_AparcAseg): No edge data
121117-19:30:55,864 workflow DEBUG:
(mapping.mri_convert_AparcAseg, mapping.inverse_AparcAseg): new edge data: {'connect': [('out_file', 'in_file')]}
121117-19:30:55,865 workflow DEBUG:
(mapping.mri_convert_AparcAseg, mapping.ROIGen_structspace): No edge data
121117-19:30:55,865 workflow DEBUG:
(mapping.mri_convert_AparcAseg, mapping.ROIGen_structspace): new edge data: {'connect': [('out_file', 'aparc_aseg_file')]}
121117-19:30:55,865 workflow DEBUG:
(mapping.ROIGen_structspace, mapping.CreateNodes): No edge data
121117-19:30:55,865 workflow DEBUG:
(mapping.ROIGen_structspace, mapping.CreateNodes): new edge data: {'connect': [('roi_file', 'roi_file')]}
121117-19:30:55,865 workflow DEBUG:
(mapping.inverse_AparcAseg, mapping.ROIGen): No edge data
121117-19:30:55,865 workflow DEBUG:
(mapping.inverse_AparcAseg, mapping.ROIGen): new edge data: {'connect': [('out_file', 'aparc_aseg_file')]}
121117-19:30:55,866 workflow DEBUG:
(mapping.ROIGen, mapping.CreateMatrix): No edge data
121117-19:30:55,866 workflow DEBUG:
(mapping.ROIGen, mapping.CreateMatrix): new edge data: {'connect': [('roi_file', 'roi_file')]}
121117-19:30:55,866 workflow DEBUG:
(mapping.camino2trackvis, mapping.CreateMatrix): No edge data
121117-19:30:55,866 workflow DEBUG:
(mapping.camino2trackvis, mapping.CreateMatrix): new edge data: {'connect': [('trackvis', 'tract_file')]}
121117-19:30:55,867 workflow DEBUG:
(mapping.inputnode_within, mapping.CreateMatrix): No edge data
121117-19:30:55,867 workflow DEBUG:
(mapping.inputnode_within, mapping.CreateMatrix): new edge data: {'connect': [('subject_id', 'out_matrix_file')]}
121117-19:30:55,867 workflow DEBUG:
(mapping.inputnode_within, mapping.CreateMatrix): Edge data exists: {'connect': [('subject_id', 'out_matrix_file')]}
121117-19:30:55,867 workflow DEBUG:
(mapping.inputnode_within, mapping.CreateMatrix): new edge data: {'connect': [('subject_id', 'out_matrix_file'), ('subject_id', 'out_matrix_mat_file')]}
121117-19:30:55,868 workflow DEBUG:
(mapping.mris_convertLH, mapping.GiftiSurfaces): No edge data
121117-19:30:55,868 workflow DEBUG:
(mapping.mris_convertLH, mapping.GiftiSurfaces): new edge data: {'connect': [('converted', 'in1')]}
121117-19:30:55,868 workflow DEBUG:
(mapping.mris_convertRH, mapping.GiftiSurfaces): No edge data
121117-19:30:55,868 workflow DEBUG:
(mapping.mris_convertRH, mapping.GiftiSurfaces): new edge data: {'connect': [('converted', 'in2')]}
121117-19:30:55,868 workflow DEBUG:
(mapping.mris_convertLHwhite, mapping.GiftiSurfaces): No edge data
121117-19:30:55,868 workflow DEBUG:
(mapping.mris_convertLHwhite, mapping.GiftiSurfaces): new edge data: {'connect': [('converted', 'in3')]}
121117-19:30:55,868 workflow DEBUG:
(mapping.mris_convertRHwhite, mapping.GiftiSurfaces): No edge data
121117-19:30:55,868 workflow DEBUG:
(mapping.mris_convertRHwhite, mapping.GiftiSurfaces): new edge data: {'connect': [('converted', 'in4')]}
121117-19:30:55,869 workflow DEBUG:
(mapping.mris_convertLHinflated, mapping.GiftiSurfaces): No edge data
121117-19:30:55,869 workflow DEBUG:
(mapping.mris_convertLHinflated, mapping.GiftiSurfaces): new edge data: {'connect': [('converted', 'in5')]}
121117-19:30:55,869 workflow DEBUG:
(mapping.mris_convertRHinflated, mapping.GiftiSurfaces): No edge data
121117-19:30:55,869 workflow DEBUG:
(mapping.mris_convertRHinflated, mapping.GiftiSurfaces): new edge data: {'connect': [('converted', 'in6')]}
121117-19:30:55,869 workflow DEBUG:
(mapping.mris_convertLHsphere, mapping.GiftiSurfaces): No edge data
121117-19:30:55,869 workflow DEBUG:
(mapping.mris_convertLHsphere, mapping.GiftiSurfaces): new edge data: {'connect': [('converted', 'in7')]}
121117-19:30:55,870 workflow DEBUG:
(mapping.mris_convertRHsphere, mapping.GiftiSurfaces): No edge data
121117-19:30:55,870 workflow DEBUG:
(mapping.mris_convertRHsphere, mapping.GiftiSurfaces): new edge data: {'connect': [('converted', 'in8')]}
121117-19:30:55,870 workflow DEBUG:
(mapping.mris_convertLHlabels, mapping.GiftiLabels): No edge data
121117-19:30:55,870 workflow DEBUG:
(mapping.mris_convertLHlabels, mapping.GiftiLabels): new edge data: {'connect': [('converted', 'in1')]}
121117-19:30:55,870 workflow DEBUG:
(mapping.mris_convertRHlabels, mapping.GiftiLabels): No edge data
121117-19:30:55,870 workflow DEBUG:
(mapping.mris_convertRHlabels, mapping.GiftiLabels): new edge data: {'connect': [('converted', 'in2')]}
121117-19:30:55,871 workflow DEBUG:
(mapping.ROIGen, mapping.NiftiVolumes): No edge data
121117-19:30:55,871 workflow DEBUG:
(mapping.ROIGen, mapping.NiftiVolumes): new edge data: {'connect': [('roi_file', 'in1')]}
121117-19:30:55,871 workflow DEBUG:
(mapping.inputnode_within, mapping.NiftiVolumes): No edge data
121117-19:30:55,871 workflow DEBUG:
(mapping.inputnode_within, mapping.NiftiVolumes): new edge data: {'connect': [('dwi', 'in2')]}
121117-19:30:55,871 workflow DEBUG:
(mapping.mri_convert_Brain, mapping.NiftiVolumes): No edge data
121117-19:30:55,872 workflow DEBUG:
(mapping.mri_convert_Brain, mapping.NiftiVolumes): new edge data: {'connect': [('out_file', 'in3')]}
121117-19:30:55,872 workflow DEBUG:
(mapping.CreateMatrix, mapping.FiberDataArrays): No edge data
121117-19:30:55,872 workflow DEBUG:
(mapping.CreateMatrix, mapping.FiberDataArrays): new edge data: {'connect': [('endpoint_file', 'in1')]}
121117-19:30:55,873 workflow DEBUG:
(mapping.CreateMatrix, mapping.FiberDataArrays): Edge data exists: {'connect': [('endpoint_file', 'in1')]}
121117-19:30:55,873 workflow DEBUG:
(mapping.CreateMatrix, mapping.FiberDataArrays): new edge data: {'connect': [('endpoint_file', 'in1'), ('endpoint_file_mm', 'in2')]}
121117-19:30:55,873 workflow DEBUG:
(mapping.CreateMatrix, mapping.FiberDataArrays): Edge data exists: {'connect': [('endpoint_file', 'in1'), ('endpoint_file_mm', 'in2')]}
121117-19:30:55,873 workflow DEBUG:
(mapping.CreateMatrix, mapping.FiberDataArrays): new edge data: {'connect': [('endpoint_file', 'in1'), ('endpoint_file_mm', 'in2'), ('fiber_length_file', 'in3')]}
121117-19:30:55,873 workflow DEBUG:
(mapping.CreateMatrix, mapping.FiberDataArrays): Edge data exists: {'connect': [('endpoint_file', 'in1'), ('endpoint_file_mm', 'in2'), ('fiber_length_file', 'in3')]}
121117-19:30:55,874 workflow DEBUG:
(mapping.CreateMatrix, mapping.FiberDataArrays): new edge data: {'connect': [('endpoint_file', 'in1'), ('endpoint_file_mm', 'in2'), ('fiber_length_file', 'in3'), ('fiber_label_file', 'in4')]}
121117-19:30:55,874 workflow DEBUG:
(mapping.GiftiSurfaces, mapping.CFFConverter): No edge data
121117-19:30:55,874 workflow DEBUG:
(mapping.GiftiSurfaces, mapping.CFFConverter): new edge data: {'connect': [('out', 'gifti_surfaces')]}
121117-19:30:55,874 workflow DEBUG:
(mapping.GiftiLabels, mapping.CFFConverter): No edge data
121117-19:30:55,874 workflow DEBUG:
(mapping.GiftiLabels, mapping.CFFConverter): new edge data: {'connect': [('out', 'gifti_labels')]}
121117-19:30:55,875 workflow DEBUG:
(mapping.CreateMatrix, mapping.CFFConverter): No edge data
121117-19:30:55,875 workflow DEBUG:
(mapping.CreateMatrix, mapping.CFFConverter): new edge data: {'connect': [('matrix_files', 'gpickled_networks')]}
121117-19:30:55,875 workflow DEBUG:
(mapping.NiftiVolumes, mapping.CFFConverter): No edge data
121117-19:30:55,875 workflow DEBUG:
(mapping.NiftiVolumes, mapping.CFFConverter): new edge data: {'connect': [('out', 'nifti_volumes')]}
121117-19:30:55,875 workflow DEBUG:
(mapping.FiberDataArrays, mapping.CFFConverter): No edge data
121117-19:30:55,875 workflow DEBUG:
(mapping.FiberDataArrays, mapping.CFFConverter): new edge data: {'connect': [('out', 'data_files')]}
121117-19:30:55,876 workflow DEBUG:
(mapping.camino2trackvis, mapping.CFFConverter): No edge data
121117-19:30:55,876 workflow DEBUG:
(mapping.camino2trackvis, mapping.CFFConverter): new edge data: {'connect': [('trackvis', 'tract_files')]}
121117-19:30:55,876 workflow DEBUG:
(mapping.inputnode_within, mapping.CFFConverter): No edge data
121117-19:30:55,876 workflow DEBUG:
(mapping.inputnode_within, mapping.CFFConverter): new edge data: {'connect': [('subject_id', 'title')]}
121117-19:30:56,175 workflow DEBUG:
(connectivity.inputnode, connectivity.mapping): No edge data
121117-19:30:56,175 workflow DEBUG:
(connectivity.inputnode, connectivity.mapping): new edge data: {'connect': [('dwi', 'inputnode_within.dwi'), ('bvals', 'inputnode_within.bvals'), ('bvecs', 'inputnode_within.bvecs'), ('subject_id', 'inputnode_within.subject_id'), ('subjects_dir', 'inputnode_within.subjects_dir'), ('resolution_network_file', 'inputnode_within.resolution_network_file')]}
121117-19:30:56,516 workflow DEBUG:
(connectivity.mapping, connectivity.outputnode): No edge data
121117-19:30:56,516 workflow DEBUG:
(connectivity.mapping, connectivity.outputnode): new edge data: {'connect': [('camino2trackvis.trackvis', 'tracts'), ('CFFConverter.connectome_file', 'connectome'), ('CreateMatrix.matrix_mat_file', 'cmatrix'), ('CreateMatrix.mean_fiber_length_matrix_mat_file', 'mean_fiber_length'), ('CreateMatrix.fiber_length_std_matrix_mat_file', 'fiber_length_std'), ('fa2nii.nifti_file', 'fa'), ('CreateMatrix.matrix_files', 'networks'), ('ROIGen.roi_file', 'rois'), ('mri_convert_Brain.out_file', 'struct'), ('trace2nii.nifti_file', 'trace'), ('dtifit.tensor_fitted', 'tensors')]}
121117-19:30:56,554 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_fsl2scheme;
121117-19:30:56,554 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_bet_b0;
121117-19:30:56,554 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_CreateMatrix;
121117-19:30:56,554 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_fssource;
121117-19:30:56,554 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_camino2trackvis;
121117-19:30:56,554 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_image2voxel;
121117-19:30:56,555 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_analyzeheader_trace;
121117-19:30:56,555 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_CFFConverter;
121117-19:30:56,555 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_CreateNodes;
121117-19:30:56,555 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_fssourceRH;
121117-19:30:56,555 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_fssourceLH;
121117-19:30:56,555 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_trace2nii;
121117-19:30:56,555 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_NiftiVolumes;
121117-19:30:56,555 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_analyzeheader_fa;
121117-19:30:56,555 workflow DEBUG:
connection: connectivity_mapping_inputnode_within -> connectivity_mapping_fa2nii;
121117-19:30:56,555 workflow DEBUG:
connection: connectivity_mapping_fssource -> connectivity_mapping_mri_convert_Brain;
121117-19:30:56,555 workflow DEBUG:
connection: connectivity_mapping_fssource -> connectivity_mapping_mri_convert_AparcAseg;
121117-19:30:56,555 workflow DEBUG:
connection: connectivity_mapping_mri_convert_Brain -> connectivity_mapping_coregister;
121117-19:30:56,556 workflow DEBUG:
connection: connectivity_mapping_mri_convert_Brain -> connectivity_mapping_inverse;
121117-19:30:56,556 workflow DEBUG:
connection: connectivity_mapping_mri_convert_Brain -> connectivity_mapping_NiftiVolumes;
121117-19:30:56,556 workflow DEBUG:
connection: connectivity_mapping_mri_convert_AparcAseg -> connectivity_mapping_inverse_AparcAseg;
121117-19:30:56,556 workflow DEBUG:
connection: connectivity_mapping_mri_convert_AparcAseg -> connectivity_mapping_ROIGen_structspace;
121117-19:30:56,556 workflow DEBUG:
connection: connectivity_mapping_image2voxel -> connectivity_mapping_dtifit;
121117-19:30:56,556 workflow DEBUG:
connection: connectivity_mapping_fsl2scheme -> connectivity_mapping_dtifit;
121117-19:30:56,556 workflow DEBUG:
connection: connectivity_mapping_fsl2scheme -> connectivity_mapping_dtlutgen;
121117-19:30:56,556 workflow DEBUG:
connection: connectivity_mapping_dtifit -> connectivity_mapping_picopdfs;
121117-19:30:56,556 workflow DEBUG:
connection: connectivity_mapping_dtifit -> connectivity_mapping_trace;
121117-19:30:56,556 workflow DEBUG:
connection: connectivity_mapping_dtifit -> connectivity_mapping_dteig;
121117-19:30:56,556 workflow DEBUG:
connection: connectivity_mapping_dtifit -> connectivity_mapping_fa;
121117-19:30:56,556 workflow DEBUG:
connection: connectivity_mapping_trace -> connectivity_mapping_analyzeheader_trace;
121117-19:30:56,556 workflow DEBUG:
connection: connectivity_mapping_trace -> connectivity_mapping_trace2nii;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_analyzeheader_trace -> connectivity_mapping_trace2nii;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_fa -> connectivity_mapping_analyzeheader_fa;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_fa -> connectivity_mapping_fa2nii;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_analyzeheader_fa -> connectivity_mapping_fa2nii;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_dtlutgen -> connectivity_mapping_picopdfs;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_picopdfs -> connectivity_mapping_track;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHsphere;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRH;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHlabels;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHwhite;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHinflated;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_mris_convertRHsphere -> connectivity_mapping_GiftiSurfaces;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_mris_convertRHlabels -> connectivity_mapping_GiftiLabels;
121117-19:30:56,557 workflow DEBUG:
connection: connectivity_mapping_mris_convertRHinflated -> connectivity_mapping_GiftiSurfaces;
121117-19:30:56,558 workflow DEBUG:
connection: connectivity_mapping_ROIGen_structspace -> connectivity_mapping_CreateNodes;
121117-19:30:56,558 workflow DEBUG:
connection: connectivity_mapping_CreateNodes -> connectivity_mapping_CreateMatrix;
121117-19:30:56,558 workflow DEBUG:
connection: connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHinflated;
121117-19:30:56,558 workflow DEBUG:
connection: connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHsphere;
121117-19:30:56,558 workflow DEBUG:
connection: connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHlabels;
121117-19:30:56,558 workflow DEBUG:
connection: connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLH;
121117-19:30:56,558 workflow DEBUG:
connection: connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHwhite;
121117-19:30:56,558 workflow DEBUG:
connection: connectivity_mapping_mris_convertLHinflated -> connectivity_mapping_GiftiSurfaces;
121117-19:30:56,558 workflow DEBUG:
connection: connectivity_mapping_mris_convertLHsphere -> connectivity_mapping_GiftiSurfaces;
121117-19:30:56,558 workflow DEBUG:
connection: connectivity_mapping_mris_convertLHlabels -> connectivity_mapping_GiftiLabels;
121117-19:30:56,558 workflow DEBUG:
connection: connectivity_mapping_GiftiLabels -> connectivity_mapping_CFFConverter;
121117-19:30:56,558 workflow DEBUG:
connection: connectivity_mapping_mris_convertLH -> connectivity_mapping_GiftiSurfaces;
121117-19:30:56,558 workflow DEBUG:
connection: connectivity_mapping_mris_convertLHwhite -> connectivity_mapping_GiftiSurfaces;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_bet_b0 -> connectivity_mapping_coregister;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_bet_b0 -> connectivity_mapping_inverse;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_bet_b0 -> connectivity_mapping_inverse_AparcAseg;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_bet_b0 -> connectivity_mapping_track;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_coregister -> connectivity_mapping_convertxfm;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_convertxfm -> connectivity_mapping_inverse_AparcAseg;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_convertxfm -> connectivity_mapping_inverse;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_inverse_AparcAseg -> connectivity_mapping_ROIGen;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_ROIGen -> connectivity_mapping_CreateMatrix;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_ROIGen -> connectivity_mapping_NiftiVolumes;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_NiftiVolumes -> connectivity_mapping_CFFConverter;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_track -> connectivity_mapping_camino2trackvis;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_track -> connectivity_mapping_vtkstreamlines;
121117-19:30:56,559 workflow DEBUG:
connection: connectivity_mapping_camino2trackvis -> connectivity_mapping_CFFConverter;
121117-19:30:56,560 workflow DEBUG:
connection: connectivity_mapping_camino2trackvis -> connectivity_mapping_trk2camino;
121117-19:30:56,560 workflow DEBUG:
connection: connectivity_mapping_camino2trackvis -> connectivity_mapping_CreateMatrix;
121117-19:30:56,560 workflow DEBUG:
connection: connectivity_mapping_CreateMatrix -> connectivity_mapping_FiberDataArrays;
121117-19:30:56,560 workflow DEBUG:
connection: connectivity_mapping_CreateMatrix -> connectivity_mapping_CFFConverter;
121117-19:30:56,560 workflow DEBUG:
connection: connectivity_mapping_FiberDataArrays -> connectivity_mapping_CFFConverter;
121117-19:30:56,560 workflow DEBUG:
connection: connectivity_mapping_mris_convertRHwhite -> connectivity_mapping_GiftiSurfaces;
121117-19:30:56,560 workflow DEBUG:
connection: connectivity_mapping_mris_convertRH -> connectivity_mapping_GiftiSurfaces;
121117-19:30:56,560 workflow DEBUG:
connection: connectivity_mapping_GiftiSurfaces -> connectivity_mapping_CFFConverter;
121117-19:30:56,561 workflow DEBUG:
cross connection: connectivity_inputnode -> connectivity_mapping_inputnode_within;
121117-19:30:56,561 workflow DEBUG:
cross connection: connectivity_inputnode -> connectivity_mapping_inputnode_within;
121117-19:30:56,561 workflow DEBUG:
cross connection: connectivity_inputnode -> connectivity_mapping_inputnode_within;
121117-19:30:56,561 workflow DEBUG:
cross connection: connectivity_inputnode -> connectivity_mapping_inputnode_within;
121117-19:30:56,561 workflow DEBUG:
cross connection: connectivity_inputnode -> connectivity_mapping_inputnode_within;
121117-19:30:56,561 workflow DEBUG:
cross connection: connectivity_inputnode -> connectivity_mapping_inputnode_within;
121117-19:30:56,561 workflow DEBUG:
cross connection: connectivity_mapping_camino2trackvis -> connectivity_outputnode;
121117-19:30:56,561 workflow DEBUG:
cross connection: connectivity_mapping_CFFConverter -> connectivity_outputnode;
121117-19:30:56,562 workflow DEBUG:
cross connection: connectivity_mapping_CreateMatrix -> connectivity_outputnode;
121117-19:30:56,562 workflow DEBUG:
cross connection: connectivity_mapping_CreateMatrix -> connectivity_outputnode;
121117-19:30:56,562 workflow DEBUG:
cross connection: connectivity_mapping_CreateMatrix -> connectivity_outputnode;
121117-19:30:56,562 workflow DEBUG:
cross connection: connectivity_mapping_fa2nii -> connectivity_outputnode;
121117-19:30:56,562 workflow DEBUG:
cross connection: connectivity_mapping_CreateMatrix -> connectivity_outputnode;
121117-19:30:56,562 workflow DEBUG:
cross connection: connectivity_mapping_ROIGen -> connectivity_outputnode;
121117-19:30:56,562 workflow DEBUG:
cross connection: connectivity_mapping_mri_convert_Brain -> connectivity_outputnode;
121117-19:30:56,562 workflow DEBUG:
cross connection: connectivity_mapping_trace2nii -> connectivity_outputnode;
121117-19:30:56,562 workflow DEBUG:
cross connection: connectivity_mapping_dtifit -> connectivity_outputnode;
121117-19:30:57,172 workflow INFO:
Converting dotfile: /var/folders/qr/mktzqkw525sfbq85mnwcrlx00000gq/T/tmpWCyHAW.dot to png format
121117-19:30:57,193 workflow DEBUG:
(tractography.inputnode1, tractography.bet): No edge data
121117-19:30:57,193 workflow DEBUG:
(tractography.inputnode1, tractography.bet): new edge data: {'connect': [('dwi', 'in_file')]}
121117-19:30:57,194 workflow DEBUG:
(tractography.inputnode1, tractography.image2voxel): No edge data
121117-19:30:57,194 workflow DEBUG:
(tractography.inputnode1, tractography.image2voxel): new edge data: {'connect': [('dwi', 'in_file')]}
121117-19:30:57,194 workflow DEBUG:
(tractography.inputnode1, tractography.fsl2scheme): No edge data
121117-19:30:57,194 workflow DEBUG:
(tractography.inputnode1, tractography.fsl2scheme): new edge data: {'connect': [('bvecs', 'bvec_file'), ('bvals', 'bval_file')]}
121117-19:30:57,195 workflow DEBUG:
(tractography.image2voxel, tractography.dtifit): No edge data
121117-19:30:57,195 workflow DEBUG:
(tractography.image2voxel, tractography.dtifit): new edge data: {'connect': [['voxel_order', 'in_file']]}
121117-19:30:57,195 workflow DEBUG:
(tractography.fsl2scheme, tractography.dtifit): No edge data
121117-19:30:57,195 workflow DEBUG:
(tractography.fsl2scheme, tractography.dtifit): new edge data: {'connect': [['scheme', 'scheme_file']]}
121117-19:30:57,195 workflow DEBUG:
(tractography.bet, tractography.trackdt): No edge data
121117-19:30:57,195 workflow DEBUG:
(tractography.bet, tractography.trackdt): new edge data: {'connect': [('mask_file', 'seed_file')]}
121117-19:30:57,196 workflow DEBUG:
(tractography.dtifit, tractography.trackdt): No edge data
121117-19:30:57,196 workflow DEBUG:
(tractography.dtifit, tractography.trackdt): new edge data: {'connect': [('tensor_fitted', 'in_file')]}
121117-19:30:57,196 workflow DEBUG:
(tractography.bet, tractography.trackpico): No edge data
121117-19:30:57,196 workflow DEBUG:
(tractography.bet, tractography.trackpico): new edge data: {'connect': [('mask_file', 'seed_file')]}
121117-19:30:57,196 workflow DEBUG:
(tractography.fsl2scheme, tractography.dtlutgen): No edge data
121117-19:30:57,196 workflow DEBUG:
(tractography.fsl2scheme, tractography.dtlutgen): new edge data: {'connect': [('scheme', 'scheme_file')]}
121117-19:30:57,196 workflow DEBUG:
(tractography.dtlutgen, tractography.picopdfs): No edge data
121117-19:30:57,196 workflow DEBUG:
(tractography.dtlutgen, tractography.picopdfs): new edge data: {'connect': [('dtLUT', 'luts')]}
121117-19:30:57,197 workflow DEBUG:
(tractography.dtifit, tractography.picopdfs): No edge data
121117-19:30:57,197 workflow DEBUG:
(tractography.dtifit, tractography.picopdfs): new edge data: {'connect': [('tensor_fitted', 'in_file')]}
121117-19:30:57,197 workflow DEBUG:
(tractography.picopdfs, tractography.trackpico): No edge data
121117-19:30:57,197 workflow DEBUG:
(tractography.picopdfs, tractography.trackpico): new edge data: {'connect': [('pdfs', 'in_file')]}
121117-19:30:57,197 workflow DEBUG:
(tractography.dtifit, tractography.fa): No edge data
121117-19:30:57,197 workflow DEBUG:
(tractography.dtifit, tractography.fa): new edge data: {'connect': [('tensor_fitted', 'in_file')]}
121117-19:30:57,197 workflow DEBUG:
(tractography.fa, tractography.analyzeheader_fa): No edge data
121117-19:30:57,198 workflow DEBUG:
(tractography.fa, tractography.analyzeheader_fa): new edge data: {'connect': [('fa', 'in_file')]}
121117-19:30:57,200 workflow DEBUG:
(tractography.inputnode1, tractography.analyzeheader_fa): No edge data
121117-19:30:57,200 workflow DEBUG:
(tractography.inputnode1, tractography.analyzeheader_fa): new edge data: {'connect': [(('dwi', "S'def get_vox_dims(volume):\\n import nibabel as nb\\n if isinstance(volume, list):\\n volume = volume[0]\\n nii = nb.load(volume)\\n hdr = nii.get_header()\\n voxdims = hdr.get_zooms()\\n return [float(voxdims[0]), float(voxdims[1]), float(voxdims[2])]\\n'\n.", ()), 'voxel_dims'), (('dwi', "S'def get_data_dims(volume):\\n import nibabel as nb\\n if isinstance(volume, list):\\n volume = volume[0]\\n nii = nb.load(volume)\\n hdr = nii.get_header()\\n datadims = hdr.get_data_shape()\\n return [int(datadims[0]), int(datadims[1]), int(datadims[2])]\\n'\n.", ()), 'data_dims')]}
121117-19:30:57,200 workflow DEBUG:
(tractography.fa, tractography.fa2nii): No edge data