interfaces.mipav.developer

JistBrainMgdmSegmentation

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainMgdmSegmentation ``.

title: MGDM Whole Brain Segmentation

category: Developer Tools

description: Estimate brain structures from an atlas for a MRI dataset (multiple input combinations are possible).

version: 2.0.RC

Inputs:

[Optional]
inMPRAGE: (an existing file name)
        MPRAGE T1-weighted Image
        argument: ``--inMPRAGE %s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
inMP2RAGE: (an existing file name)
        MP2RAGE T1 Map Image
        argument: ``--inMP2RAGE %s``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``
inPV: (an existing file name)
        PV / Dura Image
        argument: ``--inPV %s``
inCompute: ('true' or 'false')
        Compute posteriors
        argument: ``--inCompute %s``
inFLAIR: (an existing file name)
        FLAIR Image
        argument: ``--inFLAIR %s``
inData: (a float)
        Data weight
        argument: ``--inData %f``
inTopology: ('26/6' or '6/26' or '18/6' or '6/18' or '6/6' or 'wcs'
          or 'wco' or 'no')
        Topology
        argument: ``--inTopology %s``
outPosterior2: (a boolean or a file name)
        Posterior Maximum Memberships (4D)
        argument: ``--outPosterior2 %s``
outPosterior3: (a boolean or a file name)
        Posterior Maximum Labels (4D)
        argument: ``--outPosterior3 %s``
outLevelset: (a boolean or a file name)
        Levelset Boundary Image
        argument: ``--outLevelset %s``
inSteps: (an integer (int or long))
        Steps
        argument: ``--inSteps %d``
inPosterior: (a float)
        Posterior scale (mm)
        argument: ``--inPosterior %f``
inOutput: ('segmentation' or 'memberships')
        Output images
        argument: ``--inOutput %s``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
inCurvature: (a float)
        Curvature weight
        argument: ``--inCurvature %f``
inMin: (a float)
        Min change
        argument: ``--inMin %f``
inMax: (an integer (int or long))
        Max iterations
        argument: ``--inMax %d``
outSegmented: (a boolean or a file name)
        Segmented Brain Image
        argument: ``--outSegmented %s``
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
inAdjust: ('true' or 'false')
        Adjust intensity priors
        argument: ``--inAdjust %s``
inAtlas: (an existing file name)
        Atlas file
        argument: ``--inAtlas %s``
inMP2RAGE2: (an existing file name)
        MP2RAGE T1-weighted Image
        argument: ``--inMP2RAGE2 %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

Outputs:

outSegmented: (an existing file name)
        Segmented Brain Image
outPosterior2: (an existing file name)
        Posterior Maximum Memberships (4D)
outPosterior3: (an existing file name)
        Posterior Maximum Labels (4D)
outLevelset: (an existing file name)
        Levelset Boundary Image

JistBrainMp2rageDuraEstimation

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainMp2rageDuraEstimation ``.

title: MP2RAGE Dura Estimation

category: Developer Tools

description: Filters a MP2RAGE brain image to obtain a probability map of dura matter.

version: 3.0.RC

Inputs:

[Optional]
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
inSecond: (an existing file name)
        Second inversion (Inv2) Image
        argument: ``--inSecond %s``
inSkull: (an existing file name)
        Skull Stripping Mask
        argument: ``--inSkull %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
inDistance: (a float)
        Distance to background (mm)
        argument: ``--inDistance %f``
outDura: (a boolean or a file name)
        Dura Image
        argument: ``--outDura %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
null: (a unicode string)
        Execution Time
        argument: ``--null %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.
        argument: ``--inoutput %s``

Outputs:

outDura: (an existing file name)
        Dura Image

JistBrainMp2rageSkullStripping

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping ``.

title: MP2RAGE Skull Stripping

category: Developer Tools

description: Estimate a brain mask for a MP2RAGE dataset. At least a T1-weighted or a T1 map image is required.

version: 3.0.RC

Inputs:

[Optional]
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
inSecond: (an existing file name)
        Second inversion (Inv2) Image
        argument: ``--inSecond %s``
outBrain: (a boolean or a file name)
        Brain Mask Image
        argument: ``--outBrain %s``
inFilter: (an existing file name)
        Filter Image (opt)
        argument: ``--inFilter %s``
outMasked3: (a boolean or a file name)
        Masked Filter Image
        argument: ``--outMasked3 %s``
outMasked2: (a boolean or a file name)
        Masked T1-weighted Image
        argument: ``--outMasked2 %s``
outMasked: (a boolean or a file name)
        Masked T1 Map Image
        argument: ``--outMasked %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
inT1weighted: (an existing file name)
        T1-weighted (UNI) Image (opt)
        argument: ``--inT1weighted %s``
inT1: (an existing file name)
        T1 Map (T1_Images) Image (opt)
        argument: ``--inT1 %s``
inSkip: ('true' or 'false')
        Skip zero values
        argument: ``--inSkip %s``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``

Outputs:

outBrain: (an existing file name)
        Brain Mask Image
outMasked3: (an existing file name)
        Masked Filter Image
outMasked2: (an existing file name)
        Masked T1-weighted Image
outMasked: (an existing file name)
        Masked T1 Map Image

JistBrainPartialVolumeFilter

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainPartialVolumeFilter ``.

title: Partial Volume Filter

category: Developer Tools

description: Filters an image for regions of partial voluming assuming a ridge-like model of intensity.

version: 2.0.RC

Inputs:

[Optional]
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
inInput: (an existing file name)
        Input Image
        argument: ``--inInput %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
outPartial: (a boolean or a file name)
        Partial Volume Image
        argument: ``--outPartial %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
null: (a unicode string)
        Execution Time
        argument: ``--null %s``
inoutput: ('probability' or 'intensity')
        output
        argument: ``--inoutput %s``
inPV: ('bright' or 'dark' or 'both')
        Outputs the raw intensity values or a probability score for the
        partial volume regions.
        argument: ``--inPV %s``

Outputs:

outPartial: (an existing file name)
        Partial Volume Image

JistCortexSurfaceMeshInflation

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.cortex.JistCortexSurfaceMeshInflation ``.

title: Surface Mesh Inflation

category: Developer Tools

description: Inflates a cortical surface mesh. D. Tosun, M. E. Rettmann, X. Han, X. Tao, C. Xu, S. M. Resnick, D. Pham, and J. L. Prince, Cortical Surface Segmentation and Mapping, NeuroImage, vol. 23, pp. S108–S118, 2004.

version: 3.0.RC

contributor: Duygu Tosun

Inputs:

[Optional]
inMean: (a float)
        Mean Curvature Threshold
        argument: ``--inMean %f``
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
inLorentzian: ('true' or 'false')
        Lorentzian Norm
        argument: ``--inLorentzian %s``
inStep: (an integer (int or long))
        Step Size
        argument: ``--inStep %d``
outOriginal: (a boolean or a file name)
        Original Surface
        argument: ``--outOriginal %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
inLevelset: (an existing file name)
        Levelset Image
        argument: ``--inLevelset %s``
inTopology: ('26/6' or '6/26' or '18/6' or '6/18' or '6/6' or 'wcs'
          or 'wco' or 'no')
        Topology
        argument: ``--inTopology %s``
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
inSOR: (a float)
        SOR Parameter
        argument: ``--inSOR %f``
inMax: (an integer (int or long))
        Max Iterations
        argument: ``--inMax %d``
outInflated: (a boolean or a file name)
        Inflated Surface
        argument: ``--outInflated %s``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``

Outputs:

outOriginal: (an existing file name)
        Original Surface
outInflated: (an existing file name)
        Inflated Surface

JistIntensityMp2rageMasking

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.intensity.JistIntensityMp2rageMasking ``.

title: MP2RAGE Background Masking

category: Developer Tools

description: Estimate a background signal mask for a MP2RAGE dataset.

version: 3.0.RC

Inputs:

[Optional]
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
inSecond: (an existing file name)
        Second inversion (Inv2) Image
        argument: ``--inSecond %s``
inMasking: ('binary' or 'proba')
        Whether to use a binary threshold or a weighted average based on the
        probability.
        argument: ``--inMasking %s``
outSignal: (a boolean or a file name)
        Signal Proba Image
        argument: ``--outSignal_Proba %s``
inQuantitative: (an existing file name)
        Quantitative T1 Map (T1_Images) Image
        argument: ``--inQuantitative %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
inBackground: ('exponential' or 'half-normal')
        Model distribution for background noise (default is half-normal,
        exponential is more stringent).
        argument: ``--inBackground %s``
outMasked: (a boolean or a file name)
        Masked T1 Map Image
        argument: ``--outMasked_T1_Map %s``
outMasked2: (a boolean or a file name)
        Masked Iso Image
        argument: ``--outMasked_T1weighted %s``
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
inT1weighted: (an existing file name)
        T1-weighted (UNI) Image
        argument: ``--inT1weighted %s``
outSignal2: (a boolean or a file name)
        Signal Mask Image
        argument: ``--outSignal_Mask %s``
inSkip: ('true' or 'false')
        Skip zero values
        argument: ``--inSkip %s``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``

Outputs:

outSignal2: (an existing file name)
        Signal Mask Image
outSignal: (an existing file name)
        Signal Proba Image
outMasked2: (an existing file name)
        Masked Iso Image
outMasked: (an existing file name)
        Masked T1 Map Image

JistLaminarProfileCalculator

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarProfileCalculator ``.

title: Profile Calculator

category: Developer Tools

description: Compute various moments for intensities mapped along a cortical profile.

version: 3.0.RC

Inputs:

[Optional]
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
outResult: (a boolean or a file name)
        Result
        argument: ``--outResult %s``
incomputed: ('mean' or 'stdev' or 'skewness' or 'kurtosis')
        computed statistic
        argument: ``--incomputed %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
inMask: (an existing file name)
        Mask Image (opt, 3D or 4D)
        argument: ``--inMask %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
null: (a unicode string)
        Execution Time
        argument: ``--null %s``
inIntensity: (an existing file name)
        Intensity Profile Image
        argument: ``--inIntensity %s``

Outputs:

outResult: (an existing file name)
        Result

JistLaminarProfileGeometry

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarProfileGeometry ``.

title: Profile Geometry

category: Developer Tools

description: Compute various geometric quantities for a cortical layers.

version: 3.0.RC

Inputs:

[Optional]
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
incomputed: ('thickness' or 'curvedness' or 'shape_index' or
          'mean_curvature' or 'gauss_curvature' or 'profile_length' or
          'profile_curvature' or 'profile_torsion')
        computed measure
        argument: ``--incomputed %s``
outResult: (a boolean or a file name)
        Result
        argument: ``--outResult %s``
insmoothing: (a float)
        smoothing parameter
        argument: ``--insmoothing %f``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%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
inregularization: ('none' or 'Gaussian')
        regularization
        argument: ``--inregularization %s``
inoutside: (a float)
        outside extension (mm)
        argument: ``--inoutside %f``
inProfile: (an existing file name)
        Profile Surface Image
        argument: ``--inProfile %s``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``

Outputs:

outResult: (an existing file name)
        Result

JistLaminarProfileSampling

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarProfileSampling ``.

title: Profile Sampling

category: Developer Tools

description: Sample some intensity image along a cortical profile across layer surfaces.

version: 3.0.RC

Inputs:

[Optional]
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
inCortex: (an existing file name)
        Cortex Mask (opt)
        argument: ``--inCortex %s``
outProfile2: (a boolean or a file name)
        Profile 4D Mask
        argument: ``--outProfile2 %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
outProfilemapped: (a boolean or a file name)
        Profile-mapped Intensity Image
        argument: ``--outProfilemapped %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
inProfile: (an existing file name)
        Profile Surface Image
        argument: ``--inProfile %s``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``
inIntensity: (an existing file name)
        Intensity Image
        argument: ``--inIntensity %s``

Outputs:

outProfile2: (an existing file name)
        Profile 4D Mask
outProfilemapped: (an existing file name)
        Profile-mapped Intensity Image

JistLaminarROIAveraging

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarROIAveraging ``.

title: Profile ROI Averaging

category: Developer Tools

description: Compute an average profile over a given ROI.

version: 3.0.RC

Inputs:

[Optional]
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
inROI2: (a unicode string)
        ROI Name
        argument: ``--inROI2 %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
outROI3: (a boolean or a file name)
        ROI Average
        argument: ``--outROI3 %s``
inMask: (an existing file name)
        Mask Image (opt, 3D or 4D)
        argument: ``--inMask %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
inROI: (an existing file name)
        ROI Mask
        argument: ``--inROI %s``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``
inIntensity: (an existing file name)
        Intensity Profile Image
        argument: ``--inIntensity %s``

Outputs:

outROI3: (an existing file name)
        ROI Average

JistLaminarVolumetricLayering

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarVolumetricLayering ``.

title: Volumetric Layering

category: Developer Tools

description: Builds a continuous layering of the cortex following distance-preserving or volume-preserving models of cortical folding. Waehnert MD, Dinse J, Weiss M, Streicher MN, Waehnert P, Geyer S, Turner R, Bazin PL, Anatomically motivated modeling of cortical laminae, Neuroimage, 2013.

version: 3.0.RC

contributor: Miriam Waehnert (waehnert@cbs.mpg.de) http://www.cbs.mpg.de/

Inputs:

[Optional]
inLayering2: ('outward' or 'inward')
        Layering direction
        argument: ``--inLayering2 %s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
inInner: (an existing file name)
        Inner Distance Image (GM/WM boundary)
        argument: ``--inInner %s``
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
outContinuous: (a boolean or a file name)
        Continuous depth measurement
        argument: ``--outContinuous %s``
inpresmooth: ('true' or 'false')
        pre-smooth cortical surfaces
        argument: ``--inpresmooth %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
inLayering: ('distance-preserving' or 'volume-preserving')
        Layering method
        argument: ``--inLayering %s``
outDiscrete: (a boolean or a file name)
        Discrete sampled layers
        argument: ``--outDiscrete %s``
inTopology: ('26/6' or '6/26' or '18/6' or '6/18' or '6/6' or 'wcs'
          or 'wco' or 'no')
        Topology
        argument: ``--inTopology %s``
inNumber: (an integer (int or long))
        Number of layers
        argument: ``--inNumber %d``
outLayer: (a boolean or a file name)
        Layer boundary surfaces
        argument: ``--outLayer %s``
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
inMin: (a float)
        Min change ratio for narrow band evolution
        argument: ``--inMin %f``
inOuter: (an existing file name)
        Outer Distance Image (CSF/GM boundary)
        argument: ``--inOuter %s``
inMax: (an integer (int or long))
        Max iterations for narrow band evolution
        argument: ``--inMax %d``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
inratio: (a float)
        ratio smoothing kernel size (voxels)
        argument: ``--inratio %f``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``
incurvature: (an integer (int or long))
        curvature approximation scale (voxels)
        argument: ``--incurvature %d``

Outputs:

outContinuous: (an existing file name)
        Continuous depth measurement
outLayer: (an existing file name)
        Layer boundary surfaces
outDiscrete: (an existing file name)
        Discrete sampled layers

MedicAlgorithmImageCalculator

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculator ``.

title: Image Calculator

category: Developer Tools

description: Perform simple image calculator operations on two images. The operations include ‘Add’, ‘Subtract’, ‘Multiply’, and ‘Divide’

version: 1.10.RC

documentation-url: http://www.iacl.ece.jhu.edu/

Inputs:

[Optional]
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
outResult: (a boolean or a file name)
        Result Volume
        argument: ``--outResult %s``
inVolume: (an existing file name)
        Volume 1
        argument: ``--inVolume %s``
inOperation: ('Add' or 'Subtract' or 'Multiply' or 'Divide' or 'Min'
          or 'Max')
        Operation
        argument: ``--inOperation %s``
inVolume2: (an existing file name)
        Volume 2
        argument: ``--inVolume2 %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
null: (a unicode string)
        Execution Time
        argument: ``--null %s``

Outputs:

outResult: (an existing file name)
        Result Volume

MedicAlgorithmLesionToads

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmLesionToads ``.

title: Lesion TOADS

category: Developer Tools

description: Algorithm for simulataneous brain structures and MS lesion segmentation of MS Brains. The brain segmentation is topologically consistent and the algorithm can use multiple MR sequences as input data. N. Shiee, P.-L. Bazin, A.Z. Ozturk, P.A. Calabresi, D.S. Reich, D.L. Pham, “A Topology-Preserving Approach to the Segmentation of Brain Images with Multiple Sclerosis”, NeuroImage, vol. 49, no. 2, pp. 1524-1535, 2010.

version: 1.9.R

contributor: Navid Shiee (navid.shiee@nih.gov) http://iacl.ece.jhu.edu/~nshiee/

Inputs:

[Optional]
inAtlas6: ('rigid' or 'multi_fully_affine')
        Atlas alignment
        argument: ``--inAtlas6 %s``
outWM: (a boolean or a file name)
        WM Mask
        argument: ``--outWM %s``
inAtlas4: (an existing file name)
        Atlas File - No Lesion - T1 Only
        argument: ``--inAtlas4 %s``
inAtlas5: (a float)
        Controls the effect of the statistical atlas on the segmentation
        argument: ``--inAtlas5 %f``
inAtlas2: (an existing file name)
        Atlas File - With Lesions
        argument: ``--inAtlas2 %s``
inAtlas3: (an existing file name)
        Atlas File - No Lesion - T1 and FLAIR
        argument: ``--inAtlas3 %s``
inMaximum5: (an integer (int or long))
        Maximum iterations
        argument: ``--inMaximum5 %d``
inMaximum4: (a float)
        Maximum amount of relative change in the energy function considered
        as the convergence criteria
        argument: ``--inMaximum4 %f``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
inMaximum3: (an integer (int or long))
        Maximum InterVentricular Distance
        argument: ``--inMaximum3 %d``
inMaximum2: (an integer (int or long))
        Maximum Ventircle Distance
        argument: ``--inMaximum2 %d``
outHard2: (a boolean or a file name)
        Hard segmentationfrom memberships
        argument: ``--outHard2 %s``
inOutput3: ('true' or 'false')
        Output the estimated inhomogeneity field
        argument: ``--inOutput3 %s``
inOutput2: ('true' or 'false')
        Output the hard classification using maximum membership (not
        neceesarily topologically correct)
        argument: ``--inOutput2 %s``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``
outHard: (a boolean or a file name)
        Hard segmentation
        argument: ``--outHard %s``
outFilled: (a boolean or a file name)
        Filled WM Membership
        argument: ``--outFilled %s``
outMembership: (a boolean or a file name)
        Membership Functions
        argument: ``--outMembership %s``
inFLAIR: (an existing file name)
        FLAIR Image
        argument: ``--inFLAIR %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
outInhomogeneity: (a boolean or a file name)
        Inhomogeneity Field
        argument: ``--outInhomogeneity %s``
outSulcal: (a boolean or a file name)
        Sulcal CSF Membership
        argument: ``--outSulcal %s``
inOutput: ('hard segmentation' or 'hard segmentation+memberships' or
          'cruise inputs' or 'dura removal inputs')
        Output images
        argument: ``--inOutput %s``
inCorrect: ('true' or 'false')
        Correct MR field inhomogeneity.
        argument: ``--inCorrect %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
inSmooting: (a float)
        Controls the effect of neighberhood voxels on the membership
        argument: ``--inSmooting %f``
outLesion: (a boolean or a file name)
        Lesion Segmentation
        argument: ``--outLesion %s``
inConnectivity: ('(26,6)' or '(6,26)' or '(6,18)' or '(18,6)')
        Connectivity (foreground,background)
        argument: ``--inConnectivity %s``
inInclude: ('true' or 'false')
        Include lesion in WM class in hard classification
        argument: ``--inInclude %s``
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
outCortical: (a boolean or a file name)
        Cortical GM Membership
        argument: ``--outCortical %s``
inAtlas: ('With Lesion' or 'No Lesion')
        Atlas to Use
        argument: ``--inAtlas %s``
inT1_SPGR: (an existing file name)
        T1_SPGR Image
        argument: ``--inT1_SPGR %s``
inMaximum: (an integer (int or long))
        Maximum distance from the interventricular WM boundary to downweight
        the lesion membership to avoid false postives
        argument: ``--inMaximum %d``
inT1_MPRAGE: (an existing file name)
        T1_MPRAGE Image
        argument: ``--inT1_MPRAGE %s``

Outputs:

outWM: (an existing file name)
        WM Mask
outHard: (an existing file name)
        Hard segmentation
outFilled: (an existing file name)
        Filled WM Membership
outMembership: (an existing file name)
        Membership Functions
outLesion: (an existing file name)
        Lesion Segmentation
outCortical: (an existing file name)
        Cortical GM Membership
outHard2: (an existing file name)
        Hard segmentationfrom memberships
outInhomogeneity: (an existing file name)
        Inhomogeneity Field
outSulcal: (an existing file name)
        Sulcal CSF Membership

MedicAlgorithmMipavReorient

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient ``.

title: Reorient Volume

category: Developer Tools

description: Reorient a volume to a particular anatomical orientation.

version: .alpha

Inputs:

[Optional]
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
inResolution: ('Unchanged' or 'Finest cubic' or 'Coarsest cubic' or
          'Same as template')
        Resolution
        argument: ``--inResolution %s``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
inTemplate: (an existing file name)
        Template
        argument: ``--inTemplate %s``
inUser3: ('Unknown' or 'Patient Right to Left' or 'Patient Left to
          Right' or 'Patient Posterior to Anterior' or 'Patient Anterior to
          Posterior' or 'Patient Inferior to Superior' or 'Patient Superior
          to Inferior')
        User defined Z-axis orientation (into the screen)
        argument: ``--inUser3 %s``
inUser2: ('Unknown' or 'Patient Right to Left' or 'Patient Left to
          Right' or 'Patient Posterior to Anterior' or 'Patient Anterior to
          Posterior' or 'Patient Inferior to Superior' or 'Patient Superior
          to Inferior')
        User defined Y-axis orientation (image top to bottom)
        argument: ``--inUser2 %s``
outReoriented: (a list of items which are a file name)
        Reoriented Volume
        argument: ``--outReoriented %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
inInterpolation: ('Nearest Neighbor' or 'Trilinear' or 'Bspline 3rd
          order' or 'Bspline 4th order' or 'Cubic Lagrangian' or 'Quintic
          Lagrangian' or 'Heptic Lagrangian' or 'Windowed Sinc')
        Interpolation
        argument: ``--inInterpolation %s``
inUser4: ('Axial' or 'Coronal' or 'Sagittal' or 'Unknown')
        User defined Image Orientation
        argument: ``--inUser4 %s``
inNew: ('Dicom axial' or 'Dicom coronal' or 'Dicom sagittal' or 'User
          defined')
        New image orientation
        argument: ``--inNew %s``
inUser: ('Unknown' or 'Patient Right to Left' or 'Patient Left to
          Right' or 'Patient Posterior to Anterior' or 'Patient Anterior to
          Posterior' or 'Patient Inferior to Superior' or 'Patient Superior
          to Inferior')
        User defined X-axis orientation (image left to right)
        argument: ``--inUser %s``
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
inSource: (a list of items which are a file name)
        Source
        argument: ``--inSource %s``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``

Outputs:

None

MedicAlgorithmN3

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmN3 ``.

title: N3 Correction

category: Developer Tools

description: Non-parametric Intensity Non-uniformity Correction, N3, originally by J.G. Sled.

version: 1.8.R

Inputs:

[Optional]
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
inSignal: (a float)
        Default = min + 1, Values at less than threshold are treated as part
        of the background
        argument: ``--inSignal %f``
inEnd: (a float)
        Usually 0.01-0.00001, The measure used to terminate the iterations
        is the coefficient of variation of change in field estimates between
        successive iterations.
        argument: ``--inEnd %f``
inSubsample: (a float)
        Usually between 1-32, The factor by which the data is subsampled to
        a lower resolution in estimating the slowly varying non-uniformity
        field. Reduce sampling in the finest sampling direction by the
        shrink factor.
        argument: ``--inSubsample %f``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
inField: (a float)
        Characteristic distance over which the field varies. The distance
        between adjacent knots in bspline fitting with at least 4 knots
        going in every dimension. The default in the dialog is one third the
        distance (resolution * extents) of the smallest dimension.
        argument: ``--inField %f``
inWeiner: (a float)
        Usually between 0.0-1.0
        argument: ``--inWeiner %f``
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
inAutomatic: ('true' or 'false')
        If true determines the threshold by histogram analysis. If true a
        VOI cannot be used and the input threshold is ignored.
        argument: ``--inAutomatic %s``
outInhomogeneity2: (a boolean or a file name)
        Inhomogeneity Field
        argument: ``--outInhomogeneity2 %s``
outInhomogeneity: (a boolean or a file name)
        Inhomogeneity Corrected Volume
        argument: ``--outInhomogeneity %s``
inInput: (an existing file name)
        Input Volume
        argument: ``--inInput %s``
inMaximum: (an integer (int or long))
        Maximum number of Iterations
        argument: ``--inMaximum %d``
inKernel: (a float)
        Usually between 0.05-0.50, Width of deconvolution kernel used to
        sharpen the histogram. Larger values give faster convergence while
        smaller values give greater accuracy.
        argument: ``--inKernel %f``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``

Outputs:

outInhomogeneity2: (an existing file name)
        Inhomogeneity Field
outInhomogeneity: (an existing file name)
        Inhomogeneity Corrected Volume

MedicAlgorithmSPECTRE2010

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010 ``.

title: SPECTRE 2010

category: Developer Tools

description: Simple Paradigm for Extra-Cranial Tissue REmoval

Algorithm Version: 1.6 GUI Version: 1.10

A. Carass, M.B. Wheeler, J. Cuzzocreo, P.-L. Bazin, S.S. Bassett, and J.L. Prince, ‘A Joint Registration and Segmentation Approach to Skull Stripping’, Fourth IEEE International Symposium on Biomedical Imaging (ISBI 2007), Arlington, VA, April 12-15, 2007. A. Carass, J. Cuzzocreo, M.B. Wheeler, P.-L. Bazin, S.M. Resnick, and J.L. Prince, ‘Simple paradigm for extra-cerebral tissue removal: Algorithm and analysis’, NeuroImage 56(4):1982-1992, 2011.

version: 1.6.R

documentation-url: http://www.iacl.ece.jhu.edu/

contributor: Aaron Carass (aaron_carass@jhu.edu) http://www.iacl.ece.jhu.edu/ Hanlin Wan (hanlinwan@gmail.com)

Inputs:

[Optional]
inMMC2: (an integer (int or long))
        The size of the erosion step within the Modified Morphological
        Closing.
        argument: ``--inMMC2 %d``
inUse: ('true' or 'false')
        Use the max of the min resolutions of the two datasets when
        resampling
        argument: ``--inUse %s``
inSmoothing: (a float)
        argument: ``--inSmoothing %f``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
outMidsagittal: (a boolean or a file name)
        Plane dividing the brain hemispheres
        argument: ``--outMidsagittal %s``
inCost: ('Correlation ratio' or 'Least squares' or 'Normalized cross
          correlation' or 'Normalized mutual information')
        Cost function
        argument: ``--inCost %s``
inResample: ('true' or 'false')
        Determines if the data is resampled to be isotropic during the
        processing.
        argument: ``--inResample %s``
inMMC: (an integer (int or long))
        The size of the dilation step within the Modified Morphological
        Closing.
        argument: ``--inMMC %d``
inOutput3: ('true' or 'false')
        Output Split-Halves?
        argument: ``--inOutput3 %s``
inOutput2: ('true' or 'false')
        Output Plane?
        argument: ``--inOutput2 %s``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``
inFind: ('true' or 'false')
        Find Midsaggital Plane
        argument: ``--inFind %s``
inOutput5: ('Trilinear' or 'Bspline 3rd order' or 'Bspline 4th order'
          or 'Cubic Lagrangian' or 'Quintic Lagrangian' or 'Heptic
          Lagrangian' or 'Windowed sinc' or 'Nearest Neighbor')
        Output interpolation
        argument: ``--inOutput5 %s``
inOutput4: ('true' or 'false')
        Output Segmentation on Plane?
        argument: ``--inOutput4 %s``
inMultiple: (an integer (int or long))
        Multiple of tolerance to bracket the minimum
        argument: ``--inMultiple %d``
outd0: (a boolean or a file name)
        Initial Brainmask
        argument: ``--outd0 %s``
inInhomogeneity: ('true' or 'false')
        Set to false by default, this parameter will make FANTASM try to do
        inhomogeneity correction during it's iterative cycle.
        argument: ``--inInhomogeneity %s``
inSubsample: ('true' or 'false')
        Subsample image for speed
        argument: ``--inSubsample %s``
inImage: ('T1_SPGR' or 'T1_ALT' or 'T1_MPRAGE' or 'T2' or 'FLAIR')
        Set the image modality. MP-RAGE is recommended for most T1 sequence
        images.
        argument: ``--inImage %s``
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
outPrior: (a boolean or a file name)
        Probability prior from the atlas registrations
        argument: ``--outPrior %s``
inDegrees: ('Rigid - 6' or 'Global rescale - 7' or 'Specific rescale
          - 9' or 'Affine - 12')
        Degrees of freedom
        argument: ``--inDegrees %s``
outSegmentation: (a boolean or a file name)
        2D image showing the tissue classification on the midsagittal plane
        argument: ``--outSegmentation %s``
inOutput: ('true' or 'false')
        Determines if the output results are transformed back into the space
        of the original input image.
        argument: ``--inOutput %s``
inMultithreading: ('true' or 'false')
        Set to false by default, this parameter controls the multithreaded
        behavior of the linear registration.
        argument: ``--inMultithreading %s``
inMinimum: (a float)
        Minimum probability threshold
        argument: ``--inMinimum %f``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
outOriginal: (a boolean or a file name)
        If Output in Original Space Flag is true then outputs the original
        input volume. Otherwise outputs the axialy reoriented input volume.
        argument: ``--outOriginal %s``
outMask: (a boolean or a file name)
        Binary Mask of the skullstripped result with just the brain
        argument: ``--outMask %s``
inApply: ('All' or 'X' or 'Y' or 'Z')
        Apply rotation
        argument: ``--inApply %s``
inBackground: (a float)
        argument: ``--inBackground %f``
outSplitHalves: (a boolean or a file name)
        Skullstripped mask of the brain with the hemispheres divided.
        argument: ``--outSplitHalves %s``
inCoarse: (a float)
        Coarse angle increment
        argument: ``--inCoarse %f``
inNumber2: (an integer (int or long))
        Number of minima from Level 8 to test at Level 4
        argument: ``--inNumber2 %d``
inInitial: (an integer (int or long))
        Erosion of the inital mask, which is based on the probability mask
        and the classification., The initial mask is ouput as the d0 volume
        at the conclusion of SPECTRE.
        argument: ``--inInitial %d``
inSkip: ('true' or 'false')
        Skip multilevel search (Assume images are close to alignment)
        argument: ``--inSkip %s``
inFine: (a float)
        Fine angle increment
        argument: ``--inFine %f``
inMinimum2: (a float)
        Minimum angle
        argument: ``--inMinimum2 %f``
outStripped: (a boolean or a file name)
        Skullstripped result of the input volume with just the brain.
        argument: ``--outStripped %s``
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
inInitial2: (a float)
        Initial probability threshold
        argument: ``--inInitial2 %f``
inInput: (an existing file name)
        Input volume to be skullstripped.
        argument: ``--inInput %s``
inAtlas: (an existing file name)
        SPECTRE atlas description file. A text file enumerating atlas files
        and landmarks.
        argument: ``--inAtlas %s``
inRegistration: ('Trilinear' or 'Bspline 3rd order' or 'Bspline 4th
          order' or 'Cubic Lagrangian' or 'Quintic Lagrangian' or 'Heptic
          Lagrangian' or 'Windowed sinc')
        Registration interpolation
        argument: ``--inRegistration %s``
inNumber: (an integer (int or long))
        Number of iterations
        argument: ``--inNumber %d``
inMaximum: (a float)
        Maximum angle
        argument: ``--inMaximum %f``
outFANTASM: (a boolean or a file name)
        Tissue classification of of the whole input volume.
        argument: ``--outFANTASM %s``
inRun: ('true' or 'false')
        Run Smooth Brain Mask
        argument: ``--inRun %s``

Outputs:

outd0: (an existing file name)
        Initial Brainmask
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.
outMask: (an existing file name)
        Binary Mask of the skullstripped result with just the brain
outSplitHalves: (an existing file name)
        Skullstripped mask of the brain with the hemispheres divided.
outMidsagittal: (an existing file name)
        Plane dividing the brain hemispheres
outPrior: (an existing file name)
        Probability prior from the atlas registrations
outFANTASM: (an existing file name)
        Tissue classification of of the whole input volume.
outSegmentation: (an existing file name)
        2D image showing the tissue classification on the midsagittal plane
outStripped: (an existing file name)
        Skullstripped result of the input volume with just the brain.

MedicAlgorithmThresholdToBinaryMask

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThresholdToBinaryMask ``.

title: Threshold to Binary Mask

category: Developer Tools

description: Given a volume and an intensity range create a binary mask for values within that range.

version: 1.2.RC

documentation-url: http://www.iacl.ece.jhu.edu/

Inputs:

[Optional]
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
inMinimum: (a float)
        Minimum threshold value.
        argument: ``--inMinimum %f``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
inUse: ('true' or 'false')
        Use the images max intensity as the max value of the range.
        argument: ``--inUse %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
outBinary: (a list of items which are a file name)
        Binary Mask
        argument: ``--outBinary %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
inMaximum: (a float)
        Maximum threshold value.
        argument: ``--inMaximum %f``
inLabel: (a list of items which are a file name)
        Input volumes
        argument: ``--inLabel %s``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``

Outputs:

None

RandomVol

Link to code

Wraps the executable command ``java edu.jhu.ece.iacl.jist.cli.run edu.jhu.bme.smile.demo.RandomVol ``.

title: Random Volume Generator

category: Developer Tools

description: Generate a random scalar volume.

version: 1.12.RC

documentation-url: http://www.nitrc.org/projects/jist/

Inputs:

[Optional]
inStandard: (an integer (int or long))
        Standard Deviation for Normal Distribution
        argument: ``--inStandard %d``
inLambda: (a float)
        Lambda Value for Exponential Distribution
        argument: ``--inLambda %f``
xMaxProcess: (an integer (int or long), nipype default value: 1)
        Set default maximum number of processes.
        argument: ``-xMaxProcess %d``
inSize2: (an integer (int or long))
        Size of Volume in Y direction
        argument: ``--inSize2 %d``
xPrefExt: ('nrrd')
        Output File Type
        argument: ``--xPrefExt %s``
inSize4: (an integer (int or long))
        Size of Volume in t direction
        argument: ``--inSize4 %d``
xDefaultMem: (an integer (int or long))
        Set default maximum heap size
        argument: ``-xDefaultMem %d``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
inField: ('Uniform' or 'Normal' or 'Exponential')
        Field
        argument: ``--inField %s``
inSize3: (an integer (int or long))
        Size of Volume in Z direction
        argument: ``--inSize3 %d``
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
inSize: (an integer (int or long))
        Size of Volume in X direction
        argument: ``--inSize %d``
inMinimum: (an integer (int or long))
        Minimum Value
        argument: ``--inMinimum %d``
inMaximum: (an integer (int or long))
        Maximum Value
        argument: ``--inMaximum %d``
outRand1: (a boolean or a file name)
        Rand1
        argument: ``--outRand1 %s``
null: (a unicode string)
        Execution Time
        argument: ``--null %s``

Outputs:

outRand1: (an existing file name)
        Rand1