interfaces.mipav.developer

JistBrainMgdmSegmentation

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode 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: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode string)
        Execution Time
        flag: --null %s
outDura: (a boolean or a file name)
        Dura Image
        flag: --outDura %s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode 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: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode string)
        Execution Time
        flag: --null %s
outPartial: (a boolean or a file name)
        Partial Volume Image
        flag: --outPartial %s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode 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: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode 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: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode string)
        Execution Time
        flag: --null %s
outResult: (a boolean or a file name)
        Result
        flag: --outResult %s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode string)
        Execution Time
        flag: --null %s
outResult: (a boolean or a file name)
        Result
        flag: --outResult %s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode 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: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode string)
        ROI Name
        flag: --inROI2 %s
null: (a unicode string)
        Execution Time
        flag: --null %s
outROI3: (a boolean or a file name)
        ROI Average
        flag: --outROI3 %s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode 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: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode string)
        Execution Time
        flag: --null %s
outResult: (a boolean or a file name)
        Result Volume
        flag: --outResult %s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode 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: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode string)
        Execution Time
        flag: --null %s
outReoriented: (a list of items which are a file name)
        Reoriented Volume
        flag: --outReoriented %s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode 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: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode 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: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode string)
        Execution Time
        flag: --null %s
outBinary: (a list of items which are a file name)
        Binary Mask
        flag: --outBinary %s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'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

Link to code

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 unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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 unicode string)
        Execution Time
        flag: --null %s
outRand1: (a boolean or a file name)
        Rand1
        flag: --outRand1 %s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'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