.. AUTO-GENERATED FILE -- DO NOT EDIT!

interfaces.mipav.developer
==========================


.. _nipype.interfaces.mipav.developer.JistBrainMgdmSegmentation:


.. index:: JistBrainMgdmSegmentation

JistBrainMgdmSegmentation
-------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L206>`__

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

.. _nipype.interfaces.mipav.developer.JistBrainMp2rageDuraEstimation:


.. index:: JistBrainMp2rageDuraEstimation

JistBrainMp2rageDuraEstimation
------------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L974>`__

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

.. _nipype.interfaces.mipav.developer.JistBrainMp2rageSkullStripping:


.. index:: JistBrainMp2rageSkullStripping

JistBrainMp2rageSkullStripping
------------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L718>`__

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

.. _nipype.interfaces.mipav.developer.JistBrainPartialVolumeFilter:


.. index:: JistBrainPartialVolumeFilter

JistBrainPartialVolumeFilter
----------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L1458>`__

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

.. _nipype.interfaces.mipav.developer.JistCortexSurfaceMeshInflation:


.. index:: JistCortexSurfaceMeshInflation

JistCortexSurfaceMeshInflation
------------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L791>`__

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

.. _nipype.interfaces.mipav.developer.JistIntensityMp2rageMasking:


.. index:: JistIntensityMp2rageMasking

JistIntensityMp2rageMasking
---------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L1546>`__

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

.. _nipype.interfaces.mipav.developer.JistLaminarProfileCalculator:


.. index:: JistLaminarProfileCalculator

JistLaminarProfileCalculator
----------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L326>`__

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

.. _nipype.interfaces.mipav.developer.JistLaminarProfileGeometry:


.. index:: JistLaminarProfileGeometry

JistLaminarProfileGeometry
--------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L274>`__

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

.. _nipype.interfaces.mipav.developer.JistLaminarProfileSampling:


.. index:: JistLaminarProfileSampling

JistLaminarProfileSampling
--------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L1028>`__

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

.. _nipype.interfaces.mipav.developer.JistLaminarROIAveraging:


.. index:: JistLaminarROIAveraging

JistLaminarROIAveraging
-----------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L455>`__

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

.. _nipype.interfaces.mipav.developer.JistLaminarVolumetricLayering:


.. index:: JistLaminarVolumetricLayering

JistLaminarVolumetricLayering
-----------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L94>`__

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

.. _nipype.interfaces.mipav.developer.MedicAlgorithmImageCalculator:


.. index:: MedicAlgorithmImageCalculator

MedicAlgorithmImageCalculator
-----------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L914>`__

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

.. _nipype.interfaces.mipav.developer.MedicAlgorithmLesionToads:


.. index:: MedicAlgorithmLesionToads

MedicAlgorithmLesionToads
-------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L629>`__

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

.. _nipype.interfaces.mipav.developer.MedicAlgorithmMipavReorient:


.. index:: MedicAlgorithmMipavReorient

MedicAlgorithmMipavReorient
---------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L1133>`__

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

.. _nipype.interfaces.mipav.developer.MedicAlgorithmN3:


.. index:: MedicAlgorithmN3

MedicAlgorithmN3
----------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L405>`__

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

.. _nipype.interfaces.mipav.developer.MedicAlgorithmSPECTRE2010:


.. index:: MedicAlgorithmSPECTRE2010

MedicAlgorithmSPECTRE2010
-------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L1386>`__

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.

.. _nipype.interfaces.mipav.developer.MedicAlgorithmThresholdToBinaryMask:


.. index:: MedicAlgorithmThresholdToBinaryMask

MedicAlgorithmThresholdToBinaryMask
-----------------------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L1599>`__

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

.. _nipype.interfaces.mipav.developer.RandomVol:


.. index:: RandomVol

RandomVol
---------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/mipav/developer.py#L860>`__

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
