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]
inData: (a float)
Data weight
argument: ``--inData %f``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
inSteps: (an integer (int or long))
Steps
argument: ``--inSteps %d``
inMP2RAGE: (an existing file name)
MP2RAGE T1 Map Image
argument: ``--inMP2RAGE %s``
outSegmented: (a boolean or a file name)
Segmented Brain Image
argument: ``--outSegmented %s``
inCompute: ('true' or 'false')
Compute posteriors
argument: ``--inCompute %s``
inAtlas: (an existing file name)
Atlas file
argument: ``--inAtlas %s``
inPV: (an existing file name)
PV / Dura Image
argument: ``--inPV %s``
inMin: (a float)
Min change
argument: ``--inMin %f``
inCurvature: (a float)
Curvature weight
argument: ``--inCurvature %f``
outPosterior3: (a boolean or a file name)
Posterior Maximum Labels (4D)
argument: ``--outPosterior3 %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``
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
null: (a unicode string)
Execution Time
argument: ``--null %s``
inPosterior: (a float)
Posterior scale (mm)
argument: ``--inPosterior %f``
inMax: (an integer (int or long))
Max iterations
argument: ``--inMax %d``
inMPRAGE: (an existing file name)
MPRAGE T1-weighted Image
argument: ``--inMPRAGE %s``
inOutput: ('segmentation' or 'memberships')
Output images
argument: ``--inOutput %s``
inMP2RAGE2: (an existing file name)
MP2RAGE T1-weighted Image
argument: ``--inMP2RAGE2 %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outLevelset: (a boolean or a file name)
Levelset Boundary Image
argument: ``--outLevelset %s``
inFLAIR: (an existing file name)
FLAIR Image
argument: ``--inFLAIR %s``
outPosterior2: (a boolean or a file name)
Posterior Maximum Memberships (4D)
argument: ``--outPosterior2 %s``
inAdjust: ('true' or 'false')
Adjust intensity priors
argument: ``--inAdjust %s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
Outputs:
outLevelset: (an existing file name)
Levelset Boundary Image
outPosterior3: (an existing file name)
Posterior Maximum Labels (4D)
outSegmented: (an existing file name)
Segmented Brain Image
outPosterior2: (an existing file name)
Posterior Maximum Memberships (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``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
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``
null: (a unicode string)
Execution Time
argument: ``--null %s``
inDistance: (a float)
Distance to background (mm)
argument: ``--inDistance %f``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
outDura: (a boolean or a file name)
Dura Image
argument: ``--outDura %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
inSkull: (an existing file name)
Skull Stripping Mask
argument: ``--inSkull %s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
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]
inT1weighted: (an existing file name)
T1-weighted (UNI) Image (opt)
argument: ``--inT1weighted %s``
outMasked: (a boolean or a file name)
Masked T1 Map Image
argument: ``--outMasked %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
inSecond: (an existing file name)
Second inversion (Inv2) Image
argument: ``--inSecond %s``
outBrain: (a boolean or a file name)
Brain Mask Image
argument: ``--outBrain %s``
outMasked2: (a boolean or a file name)
Masked T1-weighted Image
argument: ``--outMasked2 %s``
inSkip: ('true' or 'false')
Skip zero values
argument: ``--inSkip %s``
inT1: (an existing file name)
T1 Map (T1_Images) Image (opt)
argument: ``--inT1 %s``
inFilter: (an existing file name)
Filter Image (opt)
argument: ``--inFilter %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outMasked3: (a boolean or a file name)
Masked Filter Image
argument: ``--outMasked3 %s``
null: (a unicode string)
Execution Time
argument: ``--null %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
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
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]
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
inoutput: ('probability' or 'intensity')
output
argument: ``--inoutput %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
inPV: ('bright' or 'dark' or 'both')
Outputs the raw intensity values or a probability score for the
partial volume regions.
argument: ``--inPV %s``
outPartial: (a boolean or a file name)
Partial Volume Image
argument: ``--outPartial %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
inInput: (an existing file name)
Input Image
argument: ``--inInput %s``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
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]
null: (a unicode string)
Execution Time
argument: ``--null %s``
inSOR: (a float)
SOR Parameter
argument: ``--inSOR %f``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
inMax: (an integer (int or long))
Max Iterations
argument: ``--inMax %d``
inLevelset: (an existing file name)
Levelset Image
argument: ``--inLevelset %s``
inLorentzian: ('true' or 'false')
Lorentzian Norm
argument: ``--inLorentzian %s``
outOriginal: (a boolean or a file name)
Original Surface
argument: ``--outOriginal %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
outInflated: (a boolean or a file name)
Inflated Surface
argument: ``--outInflated %s``
inMean: (a float)
Mean Curvature Threshold
argument: ``--inMean %f``
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``
inStep: (an integer (int or long))
Step Size
argument: ``--inStep %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
Outputs:
outInflated: (an existing file name)
Inflated Surface
outOriginal: (an existing file name)
Original 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]
inT1weighted: (an existing file name)
T1-weighted (UNI) Image
argument: ``--inT1weighted %s``
outMasked: (a boolean or a file name)
Masked T1 Map Image
argument: ``--outMasked_T1_Map %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
inMasking: ('binary' or 'proba')
Whether to use a binary threshold or a weighted average based on the
probability.
argument: ``--inMasking %s``
inQuantitative: (an existing file name)
Quantitative T1 Map (T1_Images) Image
argument: ``--inQuantitative %s``
null: (a unicode string)
Execution Time
argument: ``--null %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``
outSignal: (a boolean or a file name)
Signal Proba Image
argument: ``--outSignal_Proba %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
outSignal2: (a boolean or a file name)
Signal Mask Image
argument: ``--outSignal_Mask %s``
outMasked2: (a boolean or a file name)
Masked Iso Image
argument: ``--outMasked_T1weighted %s``
inSecond: (an existing file name)
Second inversion (Inv2) Image
argument: ``--inSecond %s``
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``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
Outputs:
outSignal: (an existing file name)
Signal Proba Image
outMasked: (an existing file name)
Masked T1 Map Image
outSignal2: (an existing file name)
Signal Mask 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]
null: (a unicode string)
Execution Time
argument: ``--null %s``
incomputed: ('mean' or 'stdev' or 'skewness' or 'kurtosis')
computed statistic
argument: ``--incomputed %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
outResult: (a boolean or a file name)
Result
argument: ``--outResult %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %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
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``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
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]
insmoothing: (a float)
smoothing parameter
argument: ``--insmoothing %f``
null: (a unicode string)
Execution Time
argument: ``--null %s``
inoutside: (a float)
outside extension (mm)
argument: ``--inoutside %f``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
outResult: (a boolean or a file name)
Result
argument: ``--outResult %s``
inProfile: (an existing file name)
Profile Surface Image
argument: ``--inProfile %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
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
inregularization: ('none' or 'Gaussian')
regularization
argument: ``--inregularization %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``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
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]
null: (a unicode string)
Execution Time
argument: ``--null %s``
outProfilemapped: (a boolean or a file name)
Profile-mapped Intensity Image
argument: ``--outProfilemapped %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
outProfile2: (a boolean or a file name)
Profile 4D Mask
argument: ``--outProfile2 %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %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
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``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
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]
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``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
inIntensity: (an existing file name)
Intensity Profile Image
argument: ``--inIntensity %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
inROI: (an existing file name)
ROI Mask
argument: ``--inROI %s``
inMask: (an existing file name)
Mask Image (opt, 3D or 4D)
argument: ``--inMask %s``
inROI2: (a unicode string)
ROI Name
argument: ``--inROI2 %s``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
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]
null: (a unicode string)
Execution Time
argument: ``--null %s``
inLayering2: ('outward' or 'inward')
Layering direction
argument: ``--inLayering2 %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
inLayering: ('distance-preserving' or 'volume-preserving')
Layering method
argument: ``--inLayering %s``
inMax: (an integer (int or long))
Max iterations for narrow band evolution
argument: ``--inMax %d``
inNumber: (an integer (int or long))
Number of layers
argument: ``--inNumber %d``
outLayer: (a boolean or a file name)
Layer boundary surfaces
argument: ``--outLayer %s``
inratio: (a float)
ratio smoothing kernel size (voxels)
argument: ``--inratio %f``
inOuter: (an existing file name)
Outer Distance Image (CSF/GM boundary)
argument: ``--inOuter %s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
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
inMin: (a float)
Min change ratio for narrow band evolution
argument: ``--inMin %f``
inpresmooth: ('true' or 'false')
pre-smooth cortical surfaces
argument: ``--inpresmooth %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
outContinuous: (a boolean or a file name)
Continuous depth measurement
argument: ``--outContinuous %s``
incurvature: (an integer (int or long))
curvature approximation scale (voxels)
argument: ``--incurvature %d``
outDiscrete: (a boolean or a file name)
Discrete sampled layers
argument: ``--outDiscrete %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``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
inInner: (an existing file name)
Inner Distance Image (GM/WM boundary)
argument: ``--inInner %s``
Outputs:
outLayer: (an existing file name)
Layer boundary surfaces
outDiscrete: (an existing file name)
Discrete sampled layers
outContinuous: (an existing file name)
Continuous depth measurement
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]
null: (a unicode string)
Execution Time
argument: ``--null %s``
inVolume: (an existing file name)
Volume 1
argument: ``--inVolume %s``
outResult: (a boolean or a file name)
Result Volume
argument: ``--outResult %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
inVolume2: (an existing file name)
Volume 2
argument: ``--inVolume2 %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
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
inOperation: ('Add' or 'Subtract' or 'Multiply' or 'Divide' or 'Min'
or 'Max')
Operation
argument: ``--inOperation %s``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
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]
outSulcal: (a boolean or a file name)
Sulcal CSF Membership
argument: ``--outSulcal %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
outMembership: (a boolean or a file name)
Membership Functions
argument: ``--outMembership %s``
inAtlas2: (an existing file name)
Atlas File - With Lesions
argument: ``--inAtlas2 %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
inAtlas: ('With Lesion' or 'No Lesion')
Atlas to Use
argument: ``--inAtlas %s``
inFLAIR: (an existing file name)
FLAIR Image
argument: ``--inFLAIR %s``
inInclude: ('true' or 'false')
Include lesion in WM class in hard classification
argument: ``--inInclude %s``
outFilled: (a boolean or a file name)
Filled WM Membership
argument: ``--outFilled %s``
inAtlas4: (an existing file name)
Atlas File - No Lesion - T1 Only
argument: ``--inAtlas4 %s``
inOutput3: ('true' or 'false')
Output the estimated inhomogeneity field
argument: ``--inOutput3 %s``
outWM: (a boolean or a file name)
WM Mask
argument: ``--outWM %s``
outLesion: (a boolean or a file name)
Lesion Segmentation
argument: ``--outLesion %s``
outHard: (a boolean or a file name)
Hard segmentation
argument: ``--outHard %s``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
inMaximum3: (an integer (int or long))
Maximum InterVentricular Distance
argument: ``--inMaximum3 %d``
inMaximum4: (a float)
Maximum amount of relative change in the energy function considered
as the convergence criteria
argument: ``--inMaximum4 %f``
outInhomogeneity: (a boolean or a file name)
Inhomogeneity Field
argument: ``--outInhomogeneity %s``
inAtlas5: (a float)
Controls the effect of the statistical atlas on the segmentation
argument: ``--inAtlas5 %f``
inMaximum5: (an integer (int or long))
Maximum iterations
argument: ``--inMaximum5 %d``
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``
outCortical: (a boolean or a file name)
Cortical GM Membership
argument: ``--outCortical %s``
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``
inCorrect: ('true' or 'false')
Correct MR field inhomogeneity.
argument: ``--inCorrect %s``
inT1_SPGR: (an existing file name)
T1_SPGR Image
argument: ``--inT1_SPGR %s``
inOutput: ('hard segmentation' or 'hard segmentation+memberships' or
'cruise inputs' or 'dura removal inputs')
Output images
argument: ``--inOutput %s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
inT1_MPRAGE: (an existing file name)
T1_MPRAGE Image
argument: ``--inT1_MPRAGE %s``
inOutput2: ('true' or 'false')
Output the hard classification using maximum membership (not
neceesarily topologically correct)
argument: ``--inOutput2 %s``
inAtlas3: (an existing file name)
Atlas File - No Lesion - T1 and FLAIR
argument: ``--inAtlas3 %s``
inMaximum2: (an integer (int or long))
Maximum Ventircle Distance
argument: ``--inMaximum2 %d``
inSmooting: (a float)
Controls the effect of neighberhood voxels on the membership
argument: ``--inSmooting %f``
outHard2: (a boolean or a file name)
Hard segmentationfrom memberships
argument: ``--outHard2 %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:
outSulcal: (an existing file name)
Sulcal CSF Membership
outInhomogeneity: (an existing file name)
Inhomogeneity Field
outCortical: (an existing file name)
Cortical GM Membership
outMembership: (an existing file name)
Membership Functions
outHard: (an existing file name)
Hard segmentation
outWM: (an existing file name)
WM Mask
outLesion: (an existing file name)
Lesion Segmentation
outHard2: (an existing file name)
Hard segmentationfrom memberships
outFilled: (an existing file name)
Filled WM Membership
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]
null: (a unicode string)
Execution Time
argument: ``--null %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``
inSource: (a list of items which are a file name)
Source
argument: ``--inSource %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``
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``
outReoriented: (a list of items which are a file name)
Reoriented Volume
argument: ``--outReoriented %s``
inTemplate: (an existing file name)
Template
argument: ``--inTemplate %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
inNew: ('Dicom axial' or 'Dicom coronal' or 'Dicom sagittal' or 'User
defined')
New image orientation
argument: ``--inNew %s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %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``
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
inUser4: ('Axial' or 'Coronal' or 'Sagittal' or 'Unknown')
User defined Image Orientation
argument: ``--inUser4 %s``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
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]
outInhomogeneity: (a boolean or a file name)
Inhomogeneity Corrected Volume
argument: ``--outInhomogeneity %s``
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``
inMaximum: (an integer (int or long))
Maximum number of Iterations
argument: ``--inMaximum %d``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
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``
outInhomogeneity2: (a boolean or a file name)
Inhomogeneity Field
argument: ``--outInhomogeneity2 %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
inWeiner: (a float)
Usually between 0.0-1.0
argument: ``--inWeiner %f``
inSignal: (a float)
Default = min + 1, Values at less than threshold are treated as part
of the background
argument: ``--inSignal %f``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
null: (a unicode string)
Execution Time
argument: ``--null %s``
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``
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``
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``
inInput: (an existing file name)
Input Volume
argument: ``--inInput %s``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
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]
inDegrees: ('Rigid - 6' or 'Global rescale - 7' or 'Specific rescale
- 9' or 'Affine - 12')
Degrees of freedom
argument: ``--inDegrees %s``
inApply: ('All' or 'X' or 'Y' or 'Z')
Apply rotation
argument: ``--inApply %s``
outd0: (a boolean or a file name)
Initial Brainmask
argument: ``--outd0 %s``
inBackground: (a float)
argument: ``--inBackground %f``
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``
inMultithreading: ('true' or 'false')
Set to false by default, this parameter controls the multithreaded
behavior of the linear registration.
argument: ``--inMultithreading %s``
inCoarse: (a float)
Coarse angle increment
argument: ``--inCoarse %f``
inAtlas: (an existing file name)
SPECTRE atlas description file. A text file enumerating atlas files
and landmarks.
argument: ``--inAtlas %s``
inSkip: ('true' or 'false')
Skip multilevel search (Assume images are close to alignment)
argument: ``--inSkip %s``
inMMC2: (an integer (int or long))
The size of the erosion step within the Modified Morphological
Closing.
argument: ``--inMMC2 %d``
inInitial2: (a float)
Initial probability threshold
argument: ``--inInitial2 %f``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
inSubsample: ('true' or 'false')
Subsample image for speed
argument: ``--inSubsample %s``
inMaximum: (a float)
Maximum angle
argument: ``--inMaximum %f``
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``
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``
inCost: ('Correlation ratio' or 'Least squares' or 'Normalized cross
correlation' or 'Normalized mutual information')
Cost function
argument: ``--inCost %s``
inMMC: (an integer (int or long))
The size of the dilation step within the Modified Morphological
Closing.
argument: ``--inMMC %d``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
inOutput4: ('true' or 'false')
Output Segmentation on Plane?
argument: ``--inOutput4 %s``
outSegmentation: (a boolean or a file name)
2D image showing the tissue classification on the midsagittal plane
argument: ``--outSegmentation %s``
inUse: ('true' or 'false')
Use the max of the min resolutions of the two datasets when
resampling
argument: ``--inUse %s``
inInput: (an existing file name)
Input volume to be skullstripped.
argument: ``--inInput %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
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
inNumber2: (an integer (int or long))
Number of minima from Level 8 to test at Level 4
argument: ``--inNumber2 %d``
outFANTASM: (a boolean or a file name)
Tissue classification of of the whole input volume.
argument: ``--outFANTASM %s``
null: (a unicode string)
Execution Time
argument: ``--null %s``
inSmoothing: (a float)
argument: ``--inSmoothing %f``
inRun: ('true' or 'false')
Run Smooth Brain Mask
argument: ``--inRun %s``
outMidsagittal: (a boolean or a file name)
Plane dividing the brain hemispheres
argument: ``--outMidsagittal %s``
inResample: ('true' or 'false')
Determines if the data is resampled to be isotropic during the
processing.
argument: ``--inResample %s``
inOutput3: ('true' or 'false')
Output Split-Halves?
argument: ``--inOutput3 %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``
outSplitHalves: (a boolean or a file name)
Skullstripped mask of the brain with the hemispheres divided.
argument: ``--outSplitHalves %s``
inFind: ('true' or 'false')
Find Midsaggital Plane
argument: ``--inFind %s``
inOutput2: ('true' or 'false')
Output Plane?
argument: ``--inOutput2 %s``
outPrior: (a boolean or a file name)
Probability prior from the atlas registrations
argument: ``--outPrior %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``
inNumber: (an integer (int or long))
Number of iterations
argument: ``--inNumber %d``
inFine: (a float)
Fine angle increment
argument: ``--inFine %f``
inMinimum2: (a float)
Minimum angle
argument: ``--inMinimum2 %f``
inMinimum: (a float)
Minimum probability threshold
argument: ``--inMinimum %f``
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``
inOutput: ('true' or 'false')
Determines if the output results are transformed back into the space
of the original input image.
argument: ``--inOutput %s``
inMultiple: (an integer (int or long))
Multiple of tolerance to bracket the minimum
argument: ``--inMultiple %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
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``
Outputs:
outSplitHalves: (an existing file name)
Skullstripped mask of the brain with the hemispheres divided.
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
outSegmentation: (an existing file name)
2D image showing the tissue classification on the midsagittal plane
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
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.
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]
null: (a unicode string)
Execution Time
argument: ``--null %s``
inLabel: (a list of items which are a file name)
Input volumes
argument: ``--inLabel %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
inMaximum: (a float)
Maximum threshold value.
argument: ``--inMaximum %f``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %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
inUse: ('true' or 'false')
Use the images max intensity as the max value of the range.
argument: ``--inUse %s``
inMinimum: (a float)
Minimum threshold value.
argument: ``--inMinimum %f``
outBinary: (a list of items which are a file name)
Binary Mask
argument: ``--outBinary %s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
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]
null: (a unicode string)
Execution Time
argument: ``--null %s``
xDefaultMem: (an integer (int or long))
Set default maximum heap size
argument: ``-xDefaultMem %d``
inSize4: (an integer (int or long))
Size of Volume in t direction
argument: ``--inSize4 %d``
outRand1: (a boolean or a file name)
Rand1
argument: ``--outRand1 %s``
inMaximum: (an integer (int or long))
Maximum Value
argument: ``--inMaximum %d``
inLambda: (a float)
Lambda Value for Exponential Distribution
argument: ``--inLambda %f``
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
inStandard: (an integer (int or long))
Standard Deviation for Normal Distribution
argument: ``--inStandard %d``
inSize2: (an integer (int or long))
Size of Volume in Y direction
argument: ``--inSize2 %d``
xPrefExt: ('nrrd')
Output File Type
argument: ``--xPrefExt %s``
inSize: (an integer (int or long))
Size of Volume in X direction
argument: ``--inSize %d``
inSize3: (an integer (int or long))
Size of Volume in Z direction
argument: ``--inSize3 %d``
inField: ('Uniform' or 'Normal' or 'Exponential')
Field
argument: ``--inField %s``
inMinimum: (an integer (int or long))
Minimum Value
argument: ``--inMinimum %d``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
argument: ``-xMaxProcess %d``
Outputs:
outRand1: (an existing file name)
Rand1