interfaces.mipav.developer¶
JistBrainMgdmSegmentation¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainMgdmSegmentation ``.
title: MGDM Whole Brain Segmentation
category: Developer Tools
description: Estimate brain structures from an atlas for a MRI dataset (multiple input combinations are possible).
version: 2.0.RC
Inputs:
[Optional]
inMP2RAGE: (an existing file name)
MP2RAGE T1 Map Image
argument: ``--inMP2RAGE %s``
inMP2RAGE2: (an existing file name)
MP2RAGE T1-weighted Image
argument: ``--inMP2RAGE2 %s``
inPV: (an existing file name)
PV / Dura Image
argument: ``--inPV %s``
inMPRAGE: (an existing file name)
MPRAGE T1-weighted Image
argument: ``--inMPRAGE %s``
inFLAIR: (an existing file name)
FLAIR Image
argument: ``--inFLAIR %s``
inAtlas: (an existing file name)
Atlas file
argument: ``--inAtlas %s``
inData: (a float)
Data weight
argument: ``--inData %f``
inCurvature: (a float)
Curvature weight
argument: ``--inCurvature %f``
inPosterior: (a float)
Posterior scale (mm)
argument: ``--inPosterior %f``
inMax: (an integer (int or long))
Max iterations
argument: ``--inMax %d``
inMin: (a float)
Min change
argument: ``--inMin %f``
inSteps: (an integer (int or long))
Steps
argument: ``--inSteps %d``
inTopology: ('26/6' or '6/26' or '18/6' or '6/18' or '6/6' or 'wcs'
or 'wco' or 'no')
Topology
argument: ``--inTopology %s``
inCompute: ('true' or 'false')
Compute posteriors
argument: ``--inCompute %s``
inAdjust: ('true' or 'false')
Adjust intensity priors
argument: ``--inAdjust %s``
inOutput: ('segmentation' or 'memberships')
Output images
argument: ``--inOutput %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outSegmented: (a boolean or a file name)
Segmented Brain Image
argument: ``--outSegmented %s``
outLevelset: (a boolean or a file name)
Levelset Boundary Image
argument: ``--outLevelset %s``
outPosterior2: (a boolean or a file name)
Posterior Maximum Memberships (4D)
argument: ``--outPosterior2 %s``
outPosterior3: (a boolean or a file name)
Posterior Maximum Labels (4D)
argument: ``--outPosterior3 %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outSegmented: (an existing file name)
Segmented Brain Image
outLevelset: (an existing file name)
Levelset Boundary Image
outPosterior2: (an existing file name)
Posterior Maximum Memberships (4D)
outPosterior3: (an existing file name)
Posterior Maximum Labels (4D)
JistBrainMp2rageDuraEstimation¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainMp2rageDuraEstimation ``.
title: MP2RAGE Dura Estimation
category: Developer Tools
description: Filters a MP2RAGE brain image to obtain a probability map of dura matter.
version: 3.0.RC
Inputs:
[Optional]
inSecond: (an existing file name)
Second inversion (Inv2) Image
argument: ``--inSecond %s``
inSkull: (an existing file name)
Skull Stripping Mask
argument: ``--inSkull %s``
inDistance: (a float)
Distance to background (mm)
argument: ``--inDistance %f``
inoutput: ('dura_region' or 'boundary' or 'dura_prior' or 'bg_prior'
or 'intens_prior')
Outputs an estimate of the dura / CSF boundary or an estimate of the
entire dura region.
argument: ``--inoutput %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outDura: (a boolean or a file name)
Dura Image
argument: ``--outDura %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outDura: (an existing file name)
Dura Image
JistBrainMp2rageSkullStripping¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping ``.
title: MP2RAGE Skull Stripping
category: Developer Tools
description: Estimate a brain mask for a MP2RAGE dataset. At least a T1-weighted or a T1 map image is required.
version: 3.0.RC
Inputs:
[Optional]
inSecond: (an existing file name)
Second inversion (Inv2) Image
argument: ``--inSecond %s``
inT1: (an existing file name)
T1 Map (T1_Images) Image (opt)
argument: ``--inT1 %s``
inT1weighted: (an existing file name)
T1-weighted (UNI) Image (opt)
argument: ``--inT1weighted %s``
inFilter: (an existing file name)
Filter Image (opt)
argument: ``--inFilter %s``
inSkip: ('true' or 'false')
Skip zero values
argument: ``--inSkip %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outBrain: (a boolean or a file name)
Brain Mask Image
argument: ``--outBrain %s``
outMasked: (a boolean or a file name)
Masked T1 Map Image
argument: ``--outMasked %s``
outMasked2: (a boolean or a file name)
Masked T1-weighted Image
argument: ``--outMasked2 %s``
outMasked3: (a boolean or a file name)
Masked Filter Image
argument: ``--outMasked3 %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outBrain: (an existing file name)
Brain Mask Image
outMasked: (an existing file name)
Masked T1 Map Image
outMasked2: (an existing file name)
Masked T1-weighted Image
outMasked3: (an existing file name)
Masked Filter Image
JistBrainPartialVolumeFilter¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainPartialVolumeFilter ``.
title: Partial Volume Filter
category: Developer Tools
description: Filters an image for regions of partial voluming assuming a ridge-like model of intensity.
version: 2.0.RC
Inputs:
[Optional]
inInput: (an existing file name)
Input Image
argument: ``--inInput %s``
inPV: ('bright' or 'dark' or 'both')
Outputs the raw intensity values or a probability score for the
partial volume regions.
argument: ``--inPV %s``
inoutput: ('probability' or 'intensity')
output
argument: ``--inoutput %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outPartial: (a boolean or a file name)
Partial Volume Image
argument: ``--outPartial %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outPartial: (an existing file name)
Partial Volume Image
JistCortexSurfaceMeshInflation¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.cortex.JistCortexSurfaceMeshInflation ``.
title: Surface Mesh Inflation
category: Developer Tools
description: Inflates a cortical surface mesh. D. Tosun, M. E. Rettmann, X. Han, X. Tao, C. Xu, S. M. Resnick, D. Pham, and J. L. Prince, Cortical Surface Segmentation and Mapping, NeuroImage, vol. 23, pp. S108–S118, 2004.
version: 3.0.RC
contributor: Duygu Tosun
Inputs:
[Optional]
inLevelset: (an existing file name)
Levelset Image
argument: ``--inLevelset %s``
inSOR: (a float)
SOR Parameter
argument: ``--inSOR %f``
inMean: (a float)
Mean Curvature Threshold
argument: ``--inMean %f``
inStep: (an integer (int or long))
Step Size
argument: ``--inStep %d``
inMax: (an integer (int or long))
Max Iterations
argument: ``--inMax %d``
inLorentzian: ('true' or 'false')
Lorentzian Norm
argument: ``--inLorentzian %s``
inTopology: ('26/6' or '6/26' or '18/6' or '6/18' or '6/6' or 'wcs'
or 'wco' or 'no')
Topology
argument: ``--inTopology %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outOriginal: (a boolean or a file name)
Original Surface
argument: ``--outOriginal %s``
outInflated: (a boolean or a file name)
Inflated Surface
argument: ``--outInflated %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outOriginal: (an existing file name)
Original Surface
outInflated: (an existing file name)
Inflated Surface
JistIntensityMp2rageMasking¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.intensity.JistIntensityMp2rageMasking ``.
title: MP2RAGE Background Masking
category: Developer Tools
description: Estimate a background signal mask for a MP2RAGE dataset.
version: 3.0.RC
Inputs:
[Optional]
inSecond: (an existing file name)
Second inversion (Inv2) Image
argument: ``--inSecond %s``
inQuantitative: (an existing file name)
Quantitative T1 Map (T1_Images) Image
argument: ``--inQuantitative %s``
inT1weighted: (an existing file name)
T1-weighted (UNI) Image
argument: ``--inT1weighted %s``
inBackground: ('exponential' or 'half-normal')
Model distribution for background noise (default is half-normal,
exponential is more stringent).
argument: ``--inBackground %s``
inSkip: ('true' or 'false')
Skip zero values
argument: ``--inSkip %s``
inMasking: ('binary' or 'proba')
Whether to use a binary threshold or a weighted average based on the
probability.
argument: ``--inMasking %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outSignal: (a boolean or a file name)
Signal Proba Image
argument: ``--outSignal_Proba %s``
outSignal2: (a boolean or a file name)
Signal Mask Image
argument: ``--outSignal_Mask %s``
outMasked: (a boolean or a file name)
Masked T1 Map Image
argument: ``--outMasked_T1_Map %s``
outMasked2: (a boolean or a file name)
Masked Iso Image
argument: ``--outMasked_T1weighted %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outSignal: (an existing file name)
Signal Proba Image
outSignal2: (an existing file name)
Signal Mask Image
outMasked: (an existing file name)
Masked T1 Map Image
outMasked2: (an existing file name)
Masked Iso Image
JistLaminarProfileCalculator¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarProfileCalculator ``.
title: Profile Calculator
category: Developer Tools
description: Compute various moments for intensities mapped along a cortical profile.
version: 3.0.RC
Inputs:
[Optional]
inIntensity: (an existing file name)
Intensity Profile Image
argument: ``--inIntensity %s``
inMask: (an existing file name)
Mask Image (opt, 3D or 4D)
argument: ``--inMask %s``
incomputed: ('mean' or 'stdev' or 'skewness' or 'kurtosis')
computed statistic
argument: ``--incomputed %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outResult: (a boolean or a file name)
Result
argument: ``--outResult %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outResult: (an existing file name)
Result
JistLaminarProfileGeometry¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarProfileGeometry ``.
title: Profile Geometry
category: Developer Tools
description: Compute various geometric quantities for a cortical layers.
version: 3.0.RC
Inputs:
[Optional]
inProfile: (an existing file name)
Profile Surface Image
argument: ``--inProfile %s``
incomputed: ('thickness' or 'curvedness' or 'shape_index' or
'mean_curvature' or 'gauss_curvature' or 'profile_length' or
'profile_curvature' or 'profile_torsion')
computed measure
argument: ``--incomputed %s``
inregularization: ('none' or 'Gaussian')
regularization
argument: ``--inregularization %s``
insmoothing: (a float)
smoothing parameter
argument: ``--insmoothing %f``
inoutside: (a float)
outside extension (mm)
argument: ``--inoutside %f``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outResult: (a boolean or a file name)
Result
argument: ``--outResult %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outResult: (an existing file name)
Result
JistLaminarProfileSampling¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarProfileSampling ``.
title: Profile Sampling
category: Developer Tools
description: Sample some intensity image along a cortical profile across layer surfaces.
version: 3.0.RC
Inputs:
[Optional]
inProfile: (an existing file name)
Profile Surface Image
argument: ``--inProfile %s``
inIntensity: (an existing file name)
Intensity Image
argument: ``--inIntensity %s``
inCortex: (an existing file name)
Cortex Mask (opt)
argument: ``--inCortex %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outProfilemapped: (a boolean or a file name)
Profile-mapped Intensity Image
argument: ``--outProfilemapped %s``
outProfile2: (a boolean or a file name)
Profile 4D Mask
argument: ``--outProfile2 %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outProfilemapped: (an existing file name)
Profile-mapped Intensity Image
outProfile2: (an existing file name)
Profile 4D Mask
JistLaminarROIAveraging¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarROIAveraging ``.
title: Profile ROI Averaging
category: Developer Tools
description: Compute an average profile over a given ROI.
version: 3.0.RC
Inputs:
[Optional]
inIntensity: (an existing file name)
Intensity Profile Image
argument: ``--inIntensity %s``
inROI: (an existing file name)
ROI Mask
argument: ``--inROI %s``
inROI2: (a unicode string)
ROI Name
argument: ``--inROI2 %s``
inMask: (an existing file name)
Mask Image (opt, 3D or 4D)
argument: ``--inMask %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outROI3: (a boolean or a file name)
ROI Average
argument: ``--outROI3 %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outROI3: (an existing file name)
ROI Average
JistLaminarVolumetricLayering¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarVolumetricLayering ``.
title: Volumetric Layering
category: Developer Tools
description: Builds a continuous layering of the cortex following distance-preserving or volume-preserving models of cortical folding. Waehnert MD, Dinse J, Weiss M, Streicher MN, Waehnert P, Geyer S, Turner R, Bazin PL, Anatomically motivated modeling of cortical laminae, Neuroimage, 2013.
version: 3.0.RC
contributor: Miriam Waehnert (waehnert@cbs.mpg.de) http://www.cbs.mpg.de/
Inputs:
[Optional]
inInner: (an existing file name)
Inner Distance Image (GM/WM boundary)
argument: ``--inInner %s``
inOuter: (an existing file name)
Outer Distance Image (CSF/GM boundary)
argument: ``--inOuter %s``
inNumber: (an integer (int or long))
Number of layers
argument: ``--inNumber %d``
inMax: (an integer (int or long))
Max iterations for narrow band evolution
argument: ``--inMax %d``
inMin: (a float)
Min change ratio for narrow band evolution
argument: ``--inMin %f``
inLayering: ('distance-preserving' or 'volume-preserving')
Layering method
argument: ``--inLayering %s``
inLayering2: ('outward' or 'inward')
Layering direction
argument: ``--inLayering2 %s``
incurvature: (an integer (int or long))
curvature approximation scale (voxels)
argument: ``--incurvature %d``
inratio: (a float)
ratio smoothing kernel size (voxels)
argument: ``--inratio %f``
inpresmooth: ('true' or 'false')
pre-smooth cortical surfaces
argument: ``--inpresmooth %s``
inTopology: ('26/6' or '6/26' or '18/6' or '6/18' or '6/6' or 'wcs'
or 'wco' or 'no')
Topology
argument: ``--inTopology %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outContinuous: (a boolean or a file name)
Continuous depth measurement
argument: ``--outContinuous %s``
outDiscrete: (a boolean or a file name)
Discrete sampled layers
argument: ``--outDiscrete %s``
outLayer: (a boolean or a file name)
Layer boundary surfaces
argument: ``--outLayer %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outContinuous: (an existing file name)
Continuous depth measurement
outDiscrete: (an existing file name)
Discrete sampled layers
outLayer: (an existing file name)
Layer boundary surfaces
MedicAlgorithmImageCalculator¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculator ``.
title: Image Calculator
category: Developer Tools
description: Perform simple image calculator operations on two images. The operations include ‘Add’, ‘Subtract’, ‘Multiply’, and ‘Divide’
version: 1.10.RC
documentation-url: http://www.iacl.ece.jhu.edu/
Inputs:
[Optional]
inVolume: (an existing file name)
Volume 1
argument: ``--inVolume %s``
inVolume2: (an existing file name)
Volume 2
argument: ``--inVolume2 %s``
inOperation: ('Add' or 'Subtract' or 'Multiply' or 'Divide' or 'Min'
or 'Max')
Operation
argument: ``--inOperation %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outResult: (a boolean or a file name)
Result Volume
argument: ``--outResult %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outResult: (an existing file name)
Result Volume
MedicAlgorithmLesionToads¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmLesionToads ``.
title: Lesion TOADS
category: Developer Tools
description: Algorithm for simulataneous brain structures and MS lesion segmentation of MS Brains. The brain segmentation is topologically consistent and the algorithm can use multiple MR sequences as input data. N. Shiee, P.-L. Bazin, A.Z. Ozturk, P.A. Calabresi, D.S. Reich, D.L. Pham, “A Topology-Preserving Approach to the Segmentation of Brain Images with Multiple Sclerosis”, NeuroImage, vol. 49, no. 2, pp. 1524-1535, 2010.
version: 1.9.R
contributor: Navid Shiee (navid.shiee@nih.gov) http://iacl.ece.jhu.edu/~nshiee/
Inputs:
[Optional]
inT1_MPRAGE: (an existing file name)
T1_MPRAGE Image
argument: ``--inT1_MPRAGE %s``
inT1_SPGR: (an existing file name)
T1_SPGR Image
argument: ``--inT1_SPGR %s``
inFLAIR: (an existing file name)
FLAIR Image
argument: ``--inFLAIR %s``
inAtlas: ('With Lesion' or 'No Lesion')
Atlas to Use
argument: ``--inAtlas %s``
inOutput: ('hard segmentation' or 'hard segmentation+memberships' or
'cruise inputs' or 'dura removal inputs')
Output images
argument: ``--inOutput %s``
inOutput2: ('true' or 'false')
Output the hard classification using maximum membership (not
neceesarily topologically correct)
argument: ``--inOutput2 %s``
inCorrect: ('true' or 'false')
Correct MR field inhomogeneity.
argument: ``--inCorrect %s``
inOutput3: ('true' or 'false')
Output the estimated inhomogeneity field
argument: ``--inOutput3 %s``
inAtlas2: (an existing file name)
Atlas File - With Lesions
argument: ``--inAtlas2 %s``
inAtlas3: (an existing file name)
Atlas File - No Lesion - T1 and FLAIR
argument: ``--inAtlas3 %s``
inAtlas4: (an existing file name)
Atlas File - No Lesion - T1 Only
argument: ``--inAtlas4 %s``
inMaximum: (an integer (int or long))
Maximum distance from the interventricular WM boundary to downweight
the lesion membership to avoid false postives
argument: ``--inMaximum %d``
inMaximum2: (an integer (int or long))
Maximum Ventircle Distance
argument: ``--inMaximum2 %d``
inMaximum3: (an integer (int or long))
Maximum InterVentricular Distance
argument: ``--inMaximum3 %d``
inInclude: ('true' or 'false')
Include lesion in WM class in hard classification
argument: ``--inInclude %s``
inAtlas5: (a float)
Controls the effect of the statistical atlas on the segmentation
argument: ``--inAtlas5 %f``
inSmooting: (a float)
Controls the effect of neighberhood voxels on the membership
argument: ``--inSmooting %f``
inMaximum4: (a float)
Maximum amount of relative change in the energy function considered
as the convergence criteria
argument: ``--inMaximum4 %f``
inMaximum5: (an integer (int or long))
Maximum iterations
argument: ``--inMaximum5 %d``
inAtlas6: ('rigid' or 'multi_fully_affine')
Atlas alignment
argument: ``--inAtlas6 %s``
inConnectivity: ('(26,6)' or '(6,26)' or '(6,18)' or '(18,6)')
Connectivity (foreground,background)
argument: ``--inConnectivity %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outHard: (a boolean or a file name)
Hard segmentation
argument: ``--outHard %s``
outHard2: (a boolean or a file name)
Hard segmentationfrom memberships
argument: ``--outHard2 %s``
outInhomogeneity: (a boolean or a file name)
Inhomogeneity Field
argument: ``--outInhomogeneity %s``
outMembership: (a boolean or a file name)
Membership Functions
argument: ``--outMembership %s``
outLesion: (a boolean or a file name)
Lesion Segmentation
argument: ``--outLesion %s``
outSulcal: (a boolean or a file name)
Sulcal CSF Membership
argument: ``--outSulcal %s``
outCortical: (a boolean or a file name)
Cortical GM Membership
argument: ``--outCortical %s``
outFilled: (a boolean or a file name)
Filled WM Membership
argument: ``--outFilled %s``
outWM: (a boolean or a file name)
WM Mask
argument: ``--outWM %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outHard: (an existing file name)
Hard segmentation
outHard2: (an existing file name)
Hard segmentationfrom memberships
outInhomogeneity: (an existing file name)
Inhomogeneity Field
outMembership: (an existing file name)
Membership Functions
outLesion: (an existing file name)
Lesion Segmentation
outSulcal: (an existing file name)
Sulcal CSF Membership
outCortical: (an existing file name)
Cortical GM Membership
outFilled: (an existing file name)
Filled WM Membership
outWM: (an existing file name)
WM Mask
MedicAlgorithmMipavReorient¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient ``.
title: Reorient Volume
category: Developer Tools
description: Reorient a volume to a particular anatomical orientation.
version: .alpha
Inputs:
[Optional]
inSource: (a list of items which are a file name)
Source
argument: ``--inSource %s``
inTemplate: (an existing file name)
Template
argument: ``--inTemplate %s``
inNew: ('Dicom axial' or 'Dicom coronal' or 'Dicom sagittal' or 'User
defined')
New image orientation
argument: ``--inNew %s``
inUser: ('Unknown' or 'Patient Right to Left' or 'Patient Left to
Right' or 'Patient Posterior to Anterior' or 'Patient Anterior to
Posterior' or 'Patient Inferior to Superior' or 'Patient Superior
to Inferior')
User defined X-axis orientation (image left to right)
argument: ``--inUser %s``
inUser2: ('Unknown' or 'Patient Right to Left' or 'Patient Left to
Right' or 'Patient Posterior to Anterior' or 'Patient Anterior to
Posterior' or 'Patient Inferior to Superior' or 'Patient Superior
to Inferior')
User defined Y-axis orientation (image top to bottom)
argument: ``--inUser2 %s``
inUser3: ('Unknown' or 'Patient Right to Left' or 'Patient Left to
Right' or 'Patient Posterior to Anterior' or 'Patient Anterior to
Posterior' or 'Patient Inferior to Superior' or 'Patient Superior
to Inferior')
User defined Z-axis orientation (into the screen)
argument: ``--inUser3 %s``
inUser4: ('Axial' or 'Coronal' or 'Sagittal' or 'Unknown')
User defined Image Orientation
argument: ``--inUser4 %s``
inInterpolation: ('Nearest Neighbor' or 'Trilinear' or 'Bspline 3rd
order' or 'Bspline 4th order' or 'Cubic Lagrangian' or 'Quintic
Lagrangian' or 'Heptic Lagrangian' or 'Windowed Sinc')
Interpolation
argument: ``--inInterpolation %s``
inResolution: ('Unchanged' or 'Finest cubic' or 'Coarsest cubic' or
'Same as template')
Resolution
argument: ``--inResolution %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outReoriented: (a list of items which are a file name)
Reoriented Volume
argument: ``--outReoriented %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
None
MedicAlgorithmN3¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmN3 ``.
title: N3 Correction
category: Developer Tools
description: Non-parametric Intensity Non-uniformity Correction, N3, originally by J.G. Sled.
version: 1.8.R
Inputs:
[Optional]
inInput: (an existing file name)
Input Volume
argument: ``--inInput %s``
inSignal: (a float)
Default = min + 1, Values at less than threshold are treated as part
of the background
argument: ``--inSignal %f``
inMaximum: (an integer (int or long))
Maximum number of Iterations
argument: ``--inMaximum %d``
inEnd: (a float)
Usually 0.01-0.00001, The measure used to terminate the iterations
is the coefficient of variation of change in field estimates between
successive iterations.
argument: ``--inEnd %f``
inField: (a float)
Characteristic distance over which the field varies. The distance
between adjacent knots in bspline fitting with at least 4 knots
going in every dimension. The default in the dialog is one third the
distance (resolution * extents) of the smallest dimension.
argument: ``--inField %f``
inSubsample: (a float)
Usually between 1-32, The factor by which the data is subsampled to
a lower resolution in estimating the slowly varying non-uniformity
field. Reduce sampling in the finest sampling direction by the
shrink factor.
argument: ``--inSubsample %f``
inKernel: (a float)
Usually between 0.05-0.50, Width of deconvolution kernel used to
sharpen the histogram. Larger values give faster convergence while
smaller values give greater accuracy.
argument: ``--inKernel %f``
inWeiner: (a float)
Usually between 0.0-1.0
argument: ``--inWeiner %f``
inAutomatic: ('true' or 'false')
If true determines the threshold by histogram analysis. If true a
VOI cannot be used and the input threshold is ignored.
argument: ``--inAutomatic %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outInhomogeneity: (a boolean or a file name)
Inhomogeneity Corrected Volume
argument: ``--outInhomogeneity %s``
outInhomogeneity2: (a boolean or a file name)
Inhomogeneity Field
argument: ``--outInhomogeneity2 %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outInhomogeneity: (an existing file name)
Inhomogeneity Corrected Volume
outInhomogeneity2: (an existing file name)
Inhomogeneity Field
MedicAlgorithmSPECTRE2010¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010 ``.
title: SPECTRE 2010
category: Developer Tools
description: Simple Paradigm for Extra-Cranial Tissue REmoval
Algorithm Version: 1.6 GUI Version: 1.10
A. Carass, M.B. Wheeler, J. Cuzzocreo, P.-L. Bazin, S.S. Bassett, and J.L. Prince, ‘A Joint Registration and Segmentation Approach to Skull Stripping’, Fourth IEEE International Symposium on Biomedical Imaging (ISBI 2007), Arlington, VA, April 12-15, 2007. A. Carass, J. Cuzzocreo, M.B. Wheeler, P.-L. Bazin, S.M. Resnick, and J.L. Prince, ‘Simple paradigm for extra-cerebral tissue removal: Algorithm and analysis’, NeuroImage 56(4):1982-1992, 2011.
version: 1.6.R
documentation-url: http://www.iacl.ece.jhu.edu/
contributor: Aaron Carass (aaron_carass@jhu.edu) http://www.iacl.ece.jhu.edu/ Hanlin Wan (hanlinwan@gmail.com)
Inputs:
[Optional]
inInput: (an existing file name)
Input volume to be skullstripped.
argument: ``--inInput %s``
inAtlas: (an existing file name)
SPECTRE atlas description file. A text file enumerating atlas files
and landmarks.
argument: ``--inAtlas %s``
inInitial: (an integer (int or long))
Erosion of the inital mask, which is based on the probability mask
and the classification., The initial mask is ouput as the d0 volume
at the conclusion of SPECTRE.
argument: ``--inInitial %d``
inImage: ('T1_SPGR' or 'T1_ALT' or 'T1_MPRAGE' or 'T2' or 'FLAIR')
Set the image modality. MP-RAGE is recommended for most T1 sequence
images.
argument: ``--inImage %s``
inOutput: ('true' or 'false')
Determines if the output results are transformed back into the space
of the original input image.
argument: ``--inOutput %s``
inFind: ('true' or 'false')
Find Midsaggital Plane
argument: ``--inFind %s``
inRun: ('true' or 'false')
Run Smooth Brain Mask
argument: ``--inRun %s``
inResample: ('true' or 'false')
Determines if the data is resampled to be isotropic during the
processing.
argument: ``--inResample %s``
inInitial2: (a float)
Initial probability threshold
argument: ``--inInitial2 %f``
inMinimum: (a float)
Minimum probability threshold
argument: ``--inMinimum %f``
inMMC: (an integer (int or long))
The size of the dilation step within the Modified Morphological
Closing.
argument: ``--inMMC %d``
inMMC2: (an integer (int or long))
The size of the erosion step within the Modified Morphological
Closing.
argument: ``--inMMC2 %d``
inInhomogeneity: ('true' or 'false')
Set to false by default, this parameter will make FANTASM try to do
inhomogeneity correction during it's iterative cycle.
argument: ``--inInhomogeneity %s``
inSmoothing: (a float)
argument: ``--inSmoothing %f``
inBackground: (a float)
argument: ``--inBackground %f``
inOutput2: ('true' or 'false')
Output Plane?
argument: ``--inOutput2 %s``
inOutput3: ('true' or 'false')
Output Split-Halves?
argument: ``--inOutput3 %s``
inOutput4: ('true' or 'false')
Output Segmentation on Plane?
argument: ``--inOutput4 %s``
inDegrees: ('Rigid - 6' or 'Global rescale - 7' or 'Specific rescale
- 9' or 'Affine - 12')
Degrees of freedom
argument: ``--inDegrees %s``
inCost: ('Correlation ratio' or 'Least squares' or 'Normalized cross
correlation' or 'Normalized mutual information')
Cost function
argument: ``--inCost %s``
inRegistration: ('Trilinear' or 'Bspline 3rd order' or 'Bspline 4th
order' or 'Cubic Lagrangian' or 'Quintic Lagrangian' or 'Heptic
Lagrangian' or 'Windowed sinc')
Registration interpolation
argument: ``--inRegistration %s``
inOutput5: ('Trilinear' or 'Bspline 3rd order' or 'Bspline 4th order'
or 'Cubic Lagrangian' or 'Quintic Lagrangian' or 'Heptic
Lagrangian' or 'Windowed sinc' or 'Nearest Neighbor')
Output interpolation
argument: ``--inOutput5 %s``
inApply: ('All' or 'X' or 'Y' or 'Z')
Apply rotation
argument: ``--inApply %s``
inMinimum2: (a float)
Minimum angle
argument: ``--inMinimum2 %f``
inMaximum: (a float)
Maximum angle
argument: ``--inMaximum %f``
inCoarse: (a float)
Coarse angle increment
argument: ``--inCoarse %f``
inFine: (a float)
Fine angle increment
argument: ``--inFine %f``
inMultiple: (an integer (int or long))
Multiple of tolerance to bracket the minimum
argument: ``--inMultiple %d``
inNumber: (an integer (int or long))
Number of iterations
argument: ``--inNumber %d``
inNumber2: (an integer (int or long))
Number of minima from Level 8 to test at Level 4
argument: ``--inNumber2 %d``
inUse: ('true' or 'false')
Use the max of the min resolutions of the two datasets when
resampling
argument: ``--inUse %s``
inSubsample: ('true' or 'false')
Subsample image for speed
argument: ``--inSubsample %s``
inSkip: ('true' or 'false')
Skip multilevel search (Assume images are close to alignment)
argument: ``--inSkip %s``
inMultithreading: ('true' or 'false')
Set to false by default, this parameter controls the multithreaded
behavior of the linear registration.
argument: ``--inMultithreading %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outOriginal: (a boolean or a file name)
If Output in Original Space Flag is true then outputs the original
input volume. Otherwise outputs the axialy reoriented input volume.
argument: ``--outOriginal %s``
outStripped: (a boolean or a file name)
Skullstripped result of the input volume with just the brain.
argument: ``--outStripped %s``
outMask: (a boolean or a file name)
Binary Mask of the skullstripped result with just the brain
argument: ``--outMask %s``
outPrior: (a boolean or a file name)
Probability prior from the atlas registrations
argument: ``--outPrior %s``
outFANTASM: (a boolean or a file name)
Tissue classification of of the whole input volume.
argument: ``--outFANTASM %s``
outd0: (a boolean or a file name)
Initial Brainmask
argument: ``--outd0 %s``
outMidsagittal: (a boolean or a file name)
Plane dividing the brain hemispheres
argument: ``--outMidsagittal %s``
outSplitHalves: (a boolean or a file name)
Skullstripped mask of the brain with the hemispheres divided.
argument: ``--outSplitHalves %s``
outSegmentation: (a boolean or a file name)
2D image showing the tissue classification on the midsagittal plane
argument: ``--outSegmentation %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outOriginal: (an existing file name)
If Output in Original Space Flag is true then outputs the original
input volume. Otherwise outputs the axialy reoriented input volume.
outStripped: (an existing file name)
Skullstripped result of the input volume with just the brain.
outMask: (an existing file name)
Binary Mask of the skullstripped result with just the brain
outPrior: (an existing file name)
Probability prior from the atlas registrations
outFANTASM: (an existing file name)
Tissue classification of of the whole input volume.
outd0: (an existing file name)
Initial Brainmask
outMidsagittal: (an existing file name)
Plane dividing the brain hemispheres
outSplitHalves: (an existing file name)
Skullstripped mask of the brain with the hemispheres divided.
outSegmentation: (an existing file name)
2D image showing the tissue classification on the midsagittal plane
MedicAlgorithmThresholdToBinaryMask¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThresholdToBinaryMask ``.
title: Threshold to Binary Mask
category: Developer Tools
description: Given a volume and an intensity range create a binary mask for values within that range.
version: 1.2.RC
documentation-url: http://www.iacl.ece.jhu.edu/
Inputs:
[Optional]
inLabel: (a list of items which are a file name)
Input volumes
argument: ``--inLabel %s``
inMinimum: (a float)
Minimum threshold value.
argument: ``--inMinimum %f``
inMaximum: (a float)
Maximum threshold value.
argument: ``--inMaximum %f``
inUse: ('true' or 'false')
Use the images max intensity as the max value of the range.
argument: ``--inUse %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outBinary: (a list of items which are a file name)
Binary Mask
argument: ``--outBinary %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
None
RandomVol¶
Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.bme.smile.demo.RandomVol ``.
title: Random Volume Generator
category: Developer Tools
description: Generate a random scalar volume.
version: 1.12.RC
documentation-url: http://www.nitrc.org/projects/jist/
Inputs:
[Optional]
inSize: (an integer (int or long))
Size of Volume in X direction
argument: ``--inSize %d``
inSize2: (an integer (int or long))
Size of Volume in Y direction
argument: ``--inSize2 %d``
inSize3: (an integer (int or long))
Size of Volume in Z direction
argument: ``--inSize3 %d``
inSize4: (an integer (int or long))
Size of Volume in t direction
argument: ``--inSize4 %d``
inStandard: (an integer (int or long))
Standard Deviation for Normal Distribution
argument: ``--inStandard %d``
inLambda: (a float)
Lambda Value for Exponential Distribution
argument: ``--inLambda %f``
inMaximum: (an integer (int or long))
Maximum Value
argument: ``--inMaximum %d``
inMinimum: (an integer (int or long))
Minimum Value
argument: ``--inMinimum %d``
inField: ('Uniform' or 'Normal' or 'Exponential')
Field
argument: ``--inField %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outRand1: (a boolean or a file name)
Rand1
argument: ``--outRand1 %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
outRand1: (an existing file name)
Rand1