interfaces.mipav.developer¶
JistBrainMgdmSegmentation¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inAdjust: ('true' or 'false')
Adjust intensity priors
flag: --inAdjust %s
inAtlas: (an existing file name)
Atlas file
flag: --inAtlas %s
inCompute: ('true' or 'false')
Compute posteriors
flag: --inCompute %s
inCurvature: (a float)
Curvature weight
flag: --inCurvature %f
inData: (a float)
Data weight
flag: --inData %f
inFLAIR: (an existing file name)
FLAIR Image
flag: --inFLAIR %s
inMP2RAGE: (an existing file name)
MP2RAGE T1 Map Image
flag: --inMP2RAGE %s
inMP2RAGE2: (an existing file name)
MP2RAGE T1-weighted Image
flag: --inMP2RAGE2 %s
inMPRAGE: (an existing file name)
MPRAGE T1-weighted Image
flag: --inMPRAGE %s
inMax: (an integer (int or long))
Max iterations
flag: --inMax %d
inMin: (a float)
Min change
flag: --inMin %f
inOutput: ('segmentation' or 'memberships')
Output images
flag: --inOutput %s
inPV: (an existing file name)
PV / Dura Image
flag: --inPV %s
inPosterior: (a float)
Posterior scale (mm)
flag: --inPosterior %f
inSteps: (an integer (int or long))
Steps
flag: --inSteps %d
inTopology: ('26/6' or '6/26' or '18/6' or '6/18' or '6/6' or 'wcs'
or 'wco' or 'no')
Topology
flag: --inTopology %s
null: (a string)
Execution Time
flag: --null %s
outLevelset: (a boolean or a file name)
Levelset Boundary Image
flag: --outLevelset %s
outPosterior2: (a boolean or a file name)
Posterior Maximum Memberships (4D)
flag: --outPosterior2 %s
outPosterior3: (a boolean or a file name)
Posterior Maximum Labels (4D)
flag: --outPosterior3 %s
outSegmented: (a boolean or a file name)
Segmented Brain Image
flag: --outSegmented %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
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)
outSegmented: (an existing file name)
Segmented Brain Image
JistBrainMp2rageDuraEstimation¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inDistance: (a float)
Distance to background (mm)
flag: --inDistance %f
inSecond: (an existing file name)
Second inversion (Inv2) Image
flag: --inSecond %s
inSkull: (an existing file name)
Skull Stripping Mask
flag: --inSkull %s
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.
flag: --inoutput %s
null: (a string)
Execution Time
flag: --null %s
outDura: (a boolean or a file name)
Dura Image
flag: --outDura %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
outDura: (an existing file name)
Dura Image
JistBrainMp2rageSkullStripping¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inFilter: (an existing file name)
Filter Image (opt)
flag: --inFilter %s
inSecond: (an existing file name)
Second inversion (Inv2) Image
flag: --inSecond %s
inSkip: ('true' or 'false')
Skip zero values
flag: --inSkip %s
inT1: (an existing file name)
T1 Map (T1_Images) Image (opt)
flag: --inT1 %s
inT1weighted: (an existing file name)
T1-weighted (UNI) Image (opt)
flag: --inT1weighted %s
null: (a string)
Execution Time
flag: --null %s
outBrain: (a boolean or a file name)
Brain Mask Image
flag: --outBrain %s
outMasked: (a boolean or a file name)
Masked T1 Map Image
flag: --outMasked %s
outMasked2: (a boolean or a file name)
Masked T1-weighted Image
flag: --outMasked2 %s
outMasked3: (a boolean or a file name)
Masked Filter Image
flag: --outMasked3 %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
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 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inInput: (an existing file name)
Input Image
flag: --inInput %s
inPV: ('bright' or 'dark' or 'both')
Outputs the raw intensity values or a probability score for the
partial volume regions.
flag: --inPV %s
inoutput: ('probability' or 'intensity')
output
flag: --inoutput %s
null: (a string)
Execution Time
flag: --null %s
outPartial: (a boolean or a file name)
Partial Volume Image
flag: --outPartial %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
outPartial: (an existing file name)
Partial Volume Image
JistCortexSurfaceMeshInflation¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inLevelset: (an existing file name)
Levelset Image
flag: --inLevelset %s
inLorentzian: ('true' or 'false')
Lorentzian Norm
flag: --inLorentzian %s
inMax: (an integer (int or long))
Max Iterations
flag: --inMax %d
inMean: (a float)
Mean Curvature Threshold
flag: --inMean %f
inSOR: (a float)
SOR Parameter
flag: --inSOR %f
inStep: (an integer (int or long))
Step Size
flag: --inStep %d
inTopology: ('26/6' or '6/26' or '18/6' or '6/18' or '6/6' or 'wcs'
or 'wco' or 'no')
Topology
flag: --inTopology %s
null: (a string)
Execution Time
flag: --null %s
outInflated: (a boolean or a file name)
Inflated Surface
flag: --outInflated %s
outOriginal: (a boolean or a file name)
Original Surface
flag: --outOriginal %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
outInflated: (an existing file name)
Inflated Surface
outOriginal: (an existing file name)
Original Surface
JistIntensityMp2rageMasking¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inBackground: ('exponential' or 'half-normal')
Model distribution for background noise (default is half-normal,
exponential is more stringent).
flag: --inBackground %s
inMasking: ('binary' or 'proba')
Whether to use a binary threshold or a weighted average based on the
probability.
flag: --inMasking %s
inQuantitative: (an existing file name)
Quantitative T1 Map (T1_Images) Image
flag: --inQuantitative %s
inSecond: (an existing file name)
Second inversion (Inv2) Image
flag: --inSecond %s
inSkip: ('true' or 'false')
Skip zero values
flag: --inSkip %s
inT1weighted: (an existing file name)
T1-weighted (UNI) Image
flag: --inT1weighted %s
null: (a string)
Execution Time
flag: --null %s
outMasked: (a boolean or a file name)
Masked T1 Map Image
flag: --outMasked %s
outMasked2: (a boolean or a file name)
Masked Iso Image
flag: --outMasked2 %s
outSignal: (a boolean or a file name)
Signal Proba Image
flag: --outSignal %s
outSignal2: (a boolean or a file name)
Signal Mask Image
flag: --outSignal2 %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
outMasked: (an existing file name)
Masked T1 Map Image
outMasked2: (an existing file name)
Masked Iso Image
outSignal: (an existing file name)
Signal Proba Image
outSignal2: (an existing file name)
Signal Mask Image
JistLaminarProfileCalculator¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inIntensity: (an existing file name)
Intensity Profile Image
flag: --inIntensity %s
inMask: (an existing file name)
Mask Image (opt, 3D or 4D)
flag: --inMask %s
incomputed: ('mean' or 'stdev' or 'skewness' or 'kurtosis')
computed statistic
flag: --incomputed %s
null: (a string)
Execution Time
flag: --null %s
outResult: (a boolean or a file name)
Result
flag: --outResult %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
outResult: (an existing file name)
Result
JistLaminarProfileGeometry¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inProfile: (an existing file name)
Profile Surface Image
flag: --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
flag: --incomputed %s
inoutside: (a float)
outside extension (mm)
flag: --inoutside %f
inregularization: ('none' or 'Gaussian')
regularization
flag: --inregularization %s
insmoothing: (a float)
smoothing parameter
flag: --insmoothing %f
null: (a string)
Execution Time
flag: --null %s
outResult: (a boolean or a file name)
Result
flag: --outResult %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
outResult: (an existing file name)
Result
JistLaminarProfileSampling¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inCortex: (an existing file name)
Cortex Mask (opt)
flag: --inCortex %s
inIntensity: (an existing file name)
Intensity Image
flag: --inIntensity %s
inProfile: (an existing file name)
Profile Surface Image
flag: --inProfile %s
null: (a string)
Execution Time
flag: --null %s
outProfile2: (a boolean or a file name)
Profile 4D Mask
flag: --outProfile2 %s
outProfilemapped: (a boolean or a file name)
Profile-mapped Intensity Image
flag: --outProfilemapped %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
outProfile2: (an existing file name)
Profile 4D Mask
outProfilemapped: (an existing file name)
Profile-mapped Intensity Image
JistLaminarROIAveraging¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inIntensity: (an existing file name)
Intensity Profile Image
flag: --inIntensity %s
inMask: (an existing file name)
Mask Image (opt, 3D or 4D)
flag: --inMask %s
inROI: (an existing file name)
ROI Mask
flag: --inROI %s
inROI2: (a string)
ROI Name
flag: --inROI2 %s
null: (a string)
Execution Time
flag: --null %s
outROI3: (a boolean or a file name)
ROI Average
flag: --outROI3 %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
outROI3: (an existing file name)
ROI Average
JistLaminarVolumetricLayering¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inInner: (an existing file name)
Inner Distance Image (GM/WM boundary)
flag: --inInner %s
inLayering: ('distance-preserving' or 'volume-preserving')
Layering method
flag: --inLayering %s
inLayering2: ('outward' or 'inward')
Layering direction
flag: --inLayering2 %s
inMax: (an integer (int or long))
Max iterations for narrow band evolution
flag: --inMax %d
inMin: (a float)
Min change ratio for narrow band evolution
flag: --inMin %f
inNumber: (an integer (int or long))
Number of layers
flag: --inNumber %d
inOuter: (an existing file name)
Outer Distance Image (CSF/GM boundary)
flag: --inOuter %s
inTopology: ('26/6' or '6/26' or '18/6' or '6/18' or '6/6' or 'wcs'
or 'wco' or 'no')
Topology
flag: --inTopology %s
incurvature: (an integer (int or long))
curvature approximation scale (voxels)
flag: --incurvature %d
inpresmooth: ('true' or 'false')
pre-smooth cortical surfaces
flag: --inpresmooth %s
inratio: (a float)
ratio smoothing kernel size (voxels)
flag: --inratio %f
null: (a string)
Execution Time
flag: --null %s
outContinuous: (a boolean or a file name)
Continuous depth measurement
flag: --outContinuous %s
outDiscrete: (a boolean or a file name)
Discrete sampled layers
flag: --outDiscrete %s
outLayer: (a boolean or a file name)
Layer boundary surfaces
flag: --outLayer %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
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 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inOperation: ('Add' or 'Subtract' or 'Multiply' or 'Divide' or 'Min'
or 'Max')
Operation
flag: --inOperation %s
inVolume: (an existing file name)
Volume 1
flag: --inVolume %s
inVolume2: (an existing file name)
Volume 2
flag: --inVolume2 %s
null: (a string)
Execution Time
flag: --null %s
outResult: (a boolean or a file name)
Result Volume
flag: --outResult %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
outResult: (an existing file name)
Result Volume
MedicAlgorithmLesionToads¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inAtlas: ('With Lesion' or 'No Lesion')
Atlas to Use
flag: --inAtlas %s
inAtlas2: (an existing file name)
Atlas File - With Lesions
flag: --inAtlas2 %s
inAtlas3: (an existing file name)
Atlas File - No Lesion - T1 and FLAIR
flag: --inAtlas3 %s
inAtlas4: (an existing file name)
Atlas File - No Lesion - T1 Only
flag: --inAtlas4 %s
inAtlas5: (a float)
Controls the effect of the statistical atlas on the segmentation
flag: --inAtlas5 %f
inAtlas6: ('rigid' or 'multi_fully_affine')
Atlas alignment
flag: --inAtlas6 %s
inConnectivity: ('(26,6)' or '(6,26)' or '(6,18)' or '(18,6)')
Connectivity (foreground,background)
flag: --inConnectivity %s
inCorrect: ('true' or 'false')
Correct MR field inhomogeneity.
flag: --inCorrect %s
inFLAIR: (an existing file name)
FLAIR Image
flag: --inFLAIR %s
inInclude: ('true' or 'false')
Include lesion in WM class in hard classification
flag: --inInclude %s
inMaximum: (an integer (int or long))
Maximum distance from the interventricular WM boundary to downweight
the lesion membership to avoid false postives
flag: --inMaximum %d
inMaximum2: (an integer (int or long))
Maximum Ventircle Distance
flag: --inMaximum2 %d
inMaximum3: (an integer (int or long))
Maximum InterVentricular Distance
flag: --inMaximum3 %d
inMaximum4: (a float)
Maximum amount of relative change in the energy function considered
as the convergence criteria
flag: --inMaximum4 %f
inMaximum5: (an integer (int or long))
Maximum iterations
flag: --inMaximum5 %d
inOutput: ('hard segmentation' or 'hard segmentation+memberships' or
'cruise inputs' or 'dura removal inputs')
Output images
flag: --inOutput %s
inOutput2: ('true' or 'false')
Output the hard classification using maximum membership (not
neceesarily topologically correct)
flag: --inOutput2 %s
inOutput3: ('true' or 'false')
Output the estimated inhomogeneity field
flag: --inOutput3 %s
inSmooting: (a float)
Controls the effect of neighberhood voxels on the membership
flag: --inSmooting %f
inT1_MPRAGE: (an existing file name)
T1_MPRAGE Image
flag: --inT1_MPRAGE %s
inT1_SPGR: (an existing file name)
T1_SPGR Image
flag: --inT1_SPGR %s
null: (a string)
Execution Time
flag: --null %s
outCortical: (a boolean or a file name)
Cortical GM Membership
flag: --outCortical %s
outFilled: (a boolean or a file name)
Filled WM Membership
flag: --outFilled %s
outHard: (a boolean or a file name)
Hard segmentation
flag: --outHard %s
outHard2: (a boolean or a file name)
Hard segmentationfrom memberships
flag: --outHard2 %s
outInhomogeneity: (a boolean or a file name)
Inhomogeneity Field
flag: --outInhomogeneity %s
outLesion: (a boolean or a file name)
Lesion Segmentation
flag: --outLesion %s
outMembership: (a boolean or a file name)
Membership Functions
flag: --outMembership %s
outSulcal: (a boolean or a file name)
Sulcal CSF Membership
flag: --outSulcal %s
outWM: (a boolean or a file name)
WM Mask
flag: --outWM %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
outCortical: (an existing file name)
Cortical GM Membership
outFilled: (an existing file name)
Filled WM Membership
outHard: (an existing file name)
Hard segmentation
outHard2: (an existing file name)
Hard segmentationfrom memberships
outInhomogeneity: (an existing file name)
Inhomogeneity Field
outLesion: (an existing file name)
Lesion Segmentation
outMembership: (an existing file name)
Membership Functions
outSulcal: (an existing file name)
Sulcal CSF Membership
outWM: (an existing file name)
WM Mask
MedicAlgorithmMipavReorient¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
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
flag: --inInterpolation %s
inNew: ('Dicom axial' or 'Dicom coronal' or 'Dicom sagittal' or 'User
defined')
New image orientation
flag: --inNew %s
inResolution: ('Unchanged' or 'Finest cubic' or 'Coarsest cubic' or
'Same as template')
Resolution
flag: --inResolution %s
inSource: (a list of items which are a file name)
Source
flag: --inSource %s
inTemplate: (an existing file name)
Template
flag: --inTemplate %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)
flag: --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)
flag: --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)
flag: --inUser3 %s
inUser4: ('Axial' or 'Coronal' or 'Sagittal' or 'Unknown')
User defined Image Orientation
flag: --inUser4 %s
null: (a string)
Execution Time
flag: --null %s
outReoriented: (a list of items which are a file name)
Reoriented Volume
flag: --outReoriented %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
None
MedicAlgorithmN3¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
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.
flag: --inAutomatic %s
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.
flag: --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.
flag: --inField %f
inInput: (an existing file name)
Input Volume
flag: --inInput %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.
flag: --inKernel %f
inMaximum: (an integer (int or long))
Maximum number of Iterations
flag: --inMaximum %d
inSignal: (a float)
Default = min + 1, Values at less than threshold are treated as part
of the background
flag: --inSignal %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.
flag: --inSubsample %f
inWeiner: (a float)
Usually between 0.0-1.0
flag: --inWeiner %f
null: (a string)
Execution Time
flag: --null %s
outInhomogeneity: (a boolean or a file name)
Inhomogeneity Corrected Volume
flag: --outInhomogeneity %s
outInhomogeneity2: (a boolean or a file name)
Inhomogeneity Field
flag: --outInhomogeneity2 %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
outInhomogeneity: (an existing file name)
Inhomogeneity Corrected Volume
outInhomogeneity2: (an existing file name)
Inhomogeneity Field
MedicAlgorithmSPECTRE2010¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inApply: ('All' or 'X' or 'Y' or 'Z')
Apply rotation
flag: --inApply %s
inAtlas: (an existing file name)
SPECTRE atlas description file. A text file enumerating atlas files
and landmarks.
flag: --inAtlas %s
inBackground: (a float)
flag: --inBackground %f
inCoarse: (a float)
Coarse angle increment
flag: --inCoarse %f
inCost: ('Correlation ratio' or 'Least squares' or 'Normalized cross
correlation' or 'Normalized mutual information')
Cost function
flag: --inCost %s
inDegrees: ('Rigid - 6' or 'Global rescale - 7' or 'Specific rescale
- 9' or 'Affine - 12')
Degrees of freedom
flag: --inDegrees %s
inFind: ('true' or 'false')
Find Midsaggital Plane
flag: --inFind %s
inFine: (a float)
Fine angle increment
flag: --inFine %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.
flag: --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.
flag: --inInhomogeneity %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.
flag: --inInitial %d
inInitial2: (a float)
Initial probability threshold
flag: --inInitial2 %f
inInput: (an existing file name)
Input volume to be skullstripped.
flag: --inInput %s
inMMC: (an integer (int or long))
The size of the dilation step within the Modified Morphological
Closing.
flag: --inMMC %d
inMMC2: (an integer (int or long))
The size of the erosion step within the Modified Morphological
Closing.
flag: --inMMC2 %d
inMaximum: (a float)
Maximum angle
flag: --inMaximum %f
inMinimum: (a float)
Minimum probability threshold
flag: --inMinimum %f
inMinimum2: (a float)
Minimum angle
flag: --inMinimum2 %f
inMultiple: (an integer (int or long))
Multiple of tolerance to bracket the minimum
flag: --inMultiple %d
inMultithreading: ('true' or 'false')
Set to false by default, this parameter controls the multithreaded
behavior of the linear registration.
flag: --inMultithreading %s
inNumber: (an integer (int or long))
Number of iterations
flag: --inNumber %d
inNumber2: (an integer (int or long))
Number of minima from Level 8 to test at Level 4
flag: --inNumber2 %d
inOutput: ('true' or 'false')
Determines if the output results are transformed back into the space
of the original input image.
flag: --inOutput %s
inOutput2: ('true' or 'false')
Output Plane?
flag: --inOutput2 %s
inOutput3: ('true' or 'false')
Output Split-Halves?
flag: --inOutput3 %s
inOutput4: ('true' or 'false')
Output Segmentation on Plane?
flag: --inOutput4 %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
flag: --inOutput5 %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
flag: --inRegistration %s
inResample: ('true' or 'false')
Determines if the data is resampled to be isotropic during the
processing.
flag: --inResample %s
inRun: ('true' or 'false')
Run Smooth Brain Mask
flag: --inRun %s
inSkip: ('true' or 'false')
Skip multilevel search (Assume images are close to alignment)
flag: --inSkip %s
inSmoothing: (a float)
flag: --inSmoothing %f
inSubsample: ('true' or 'false')
Subsample image for speed
flag: --inSubsample %s
inUse: ('true' or 'false')
Use the max of the min resolutions of the two datasets when
resampling
flag: --inUse %s
null: (a string)
Execution Time
flag: --null %s
outFANTASM: (a boolean or a file name)
Tissue classification of of the whole input volume.
flag: --outFANTASM %s
outMask: (a boolean or a file name)
Binary Mask of the skullstripped result with just the brain
flag: --outMask %s
outMidsagittal: (a boolean or a file name)
Plane dividing the brain hemispheres
flag: --outMidsagittal %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.
flag: --outOriginal %s
outPrior: (a boolean or a file name)
Probability prior from the atlas registrations
flag: --outPrior %s
outSegmentation: (a boolean or a file name)
2D image showing the tissue classification on the midsagittal plane
flag: --outSegmentation %s
outSplitHalves: (a boolean or a file name)
Skullstripped mask of the brain with the hemispheres divided.
flag: --outSplitHalves %s
outStripped: (a boolean or a file name)
Skullstripped result of the input volume with just the brain.
flag: --outStripped %s
outd0: (a boolean or a file name)
Initial Brainmask
flag: --outd0 %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
outFANTASM: (an existing file name)
Tissue classification of of the whole input volume.
outMask: (an existing file name)
Binary Mask of the skullstripped result with just the brain
outMidsagittal: (an existing file name)
Plane dividing the brain hemispheres
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.
outPrior: (an existing file name)
Probability prior from the atlas registrations
outSegmentation: (an existing file name)
2D image showing the tissue classification on the midsagittal plane
outSplitHalves: (an existing file name)
Skullstripped mask of the brain with the hemispheres divided.
outStripped: (an existing file name)
Skullstripped result of the input volume with just the brain.
outd0: (an existing file name)
Initial Brainmask
MedicAlgorithmThresholdToBinaryMask¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inLabel: (a list of items which are a file name)
Input volumes
flag: --inLabel %s
inMaximum: (a float)
Maximum threshold value.
flag: --inMaximum %f
inMinimum: (a float)
Minimum threshold value.
flag: --inMinimum %f
inUse: ('true' or 'false')
Use the images max intensity as the max value of the range.
flag: --inUse %s
null: (a string)
Execution Time
flag: --null %s
outBinary: (a list of items which are a file name)
Binary Mask
flag: --outBinary %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
None
RandomVol¶
Wraps 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:
[Mandatory]
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inField: ('Uniform' or 'Normal' or 'Exponential')
Field
flag: --inField %s
inLambda: (a float)
Lambda Value for Exponential Distribution
flag: --inLambda %f
inMaximum: (an integer (int or long))
Maximum Value
flag: --inMaximum %d
inMinimum: (an integer (int or long))
Minimum Value
flag: --inMinimum %d
inSize: (an integer (int or long))
Size of Volume in X direction
flag: --inSize %d
inSize2: (an integer (int or long))
Size of Volume in Y direction
flag: --inSize2 %d
inSize3: (an integer (int or long))
Size of Volume in Z direction
flag: --inSize3 %d
inSize4: (an integer (int or long))
Size of Volume in t direction
flag: --inSize4 %d
inStandard: (an integer (int or long))
Standard Deviation for Normal Distribution
flag: --inStandard %d
null: (a string)
Execution Time
flag: --null %s
outRand1: (a boolean or a file name)
Rand1
flag: --outRand1 %s
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
xDefaultMem: (an integer (int or long))
Set default maximum heap size
flag: -xDefaultMem %d
xMaxProcess: (an integer (int or long), nipype default value: 1)
Set default maximum number of processes.
flag: -xMaxProcess %d
xPrefExt: ('nrrd')
Output File Type
flag: --xPrefExt %s
Outputs:
outRand1: (an existing file name)
Rand1