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# nipype.interfaces.mipav.developer module

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## JistBrainMgdmSegmentation

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainMgdmSegmentation`.

> MGDM Whole Brain Segmentation.

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

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inAdjust‘true’ or ‘false’

>   Adjust intensity priors. Maps to a command-line argument: `--inAdjust %s`.

> inAtlasa pathlike object or string representing an existing file

>   Atlas file. Maps to a command-line argument: `--inAtlas %s`.

> inCompute‘true’ or ‘false’

>   Compute posteriors. Maps to a command-line argument: `--inCompute %s`.

> inCurvaturea float

>   Curvature weight. Maps to a command-line argument: `--inCurvature %f`.

> inDataa float

>   Data weight. Maps to a command-line argument: `--inData %f`.

> inFLAIRa pathlike object or string representing an existing file

>   FLAIR Image. Maps to a command-line argument: `--inFLAIR %s`.

> inMP2RAGEa pathlike object or string representing an existing file

>   MP2RAGE T1 Map Image. Maps to a command-line argument: `--inMP2RAGE %s`.

> inMP2RAGE2a pathlike object or string representing an existing file

>   MP2RAGE T1-weighted Image. Maps to a command-line argument: `--inMP2RAGE2 %s`.

> inMPRAGEa pathlike object or string representing an existing file

>   MPRAGE T1-weighted Image. Maps to a command-line argument: `--inMPRAGE %s`.

> inMaxan integer

>   Max iterations. Maps to a command-line argument: `--inMax %d`.

> inMina float

>   Min change. Maps to a command-line argument: `--inMin %f`.

> inOutput‘segmentation’ or ‘memberships’

>   Output images. Maps to a command-line argument: `--inOutput %s`.

> inPVa pathlike object or string representing an existing file

>   PV / Dura Image. Maps to a command-line argument: `--inPV %s`.

> inPosteriora float

>   Posterior scale (mm). Maps to a command-line argument: `--inPosterior %f`.

> inStepsan integer

>   Steps. Maps to a command-line argument: `--inSteps %d`.

> inTopology‘26/6’ or ‘6/26’ or ‘18/6’ or ‘6/18’ or ‘6/6’ or ‘wcs’ or ‘wco’ or ‘no’

>   Topology. Maps to a command-line argument: `--inTopology %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outLevelseta boolean or a pathlike object or string representing a file

>   Levelset Boundary Image. Maps to a command-line argument: `--outLevelset %s`.

> outPosterior2a boolean or a pathlike object or string representing a file

>   Posterior Maximum Memberships (4D). Maps to a command-line argument: `--outPosterior2 %s`.

> outPosterior3a boolean or a pathlike object or string representing a file

>   Posterior Maximum Labels (4D). Maps to a command-line argument: `--outPosterior3 %s`.

> outSegmenteda boolean or a pathlike object or string representing a file

>   Segmented Brain Image. Maps to a command-line argument: `--outSegmented %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outLevelseta pathlike object or string representing an existing file

>   Levelset Boundary Image.

> outPosterior2a pathlike object or string representing an existing file

>   Posterior Maximum Memberships (4D).

> outPosterior3a pathlike object or string representing an existing file

>   Posterior Maximum Labels (4D).

> outSegmenteda pathlike object or string representing an existing file

>   Segmented Brain Image.

## JistBrainMp2rageDuraEstimation

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainMp2rageDuraEstimation`.

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

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inDistancea float

>   Distance to background (mm). Maps to a command-line argument: `--inDistance %f`.

> inSeconda pathlike object or string representing an existing file

>   Second inversion (Inv2) Image. Maps to a command-line argument: `--inSecond %s`.

> inSkulla pathlike object or string representing an existing file

>   Skull Stripping Mask. Maps to a command-line argument: `--inSkull %s`.

> inoutput‘dura_region’ or ‘boundary’ or ‘dura_prior’ or ‘bg_prior’ or ‘intens_prior’

>   Outputs an estimate of the dura / CSF boundary or an estimate of the entire dura region. Maps to a command-line argument: `--inoutput %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outDuraa boolean or a pathlike object or string representing a file

>   Dura Image. Maps to a command-line argument: `--outDura %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outDuraa pathlike object or string representing an existing file

>   Dura Image.

## JistBrainMp2rageSkullStripping

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping`.

> Estimate a brain mask for a MP2RAGE dataset.

> At least a T1-weighted or a T1 map image is required.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inFiltera pathlike object or string representing an existing file

>   Filter Image (opt). Maps to a command-line argument: `--inFilter %s`.

> inSeconda pathlike object or string representing an existing file

>   Second inversion (Inv2) Image. Maps to a command-line argument: `--inSecond %s`.

> inSkip‘true’ or ‘false’

>   Skip zero values. Maps to a command-line argument: `--inSkip %s`.

> inT1a pathlike object or string representing an existing file

>   T1 Map (T1_Images) Image (opt). Maps to a command-line argument: `--inT1 %s`.

> inT1weighteda pathlike object or string representing an existing file

>   T1-weighted (UNI) Image (opt). Maps to a command-line argument: `--inT1weighted %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outBraina boolean or a pathlike object or string representing a file

>   Brain Mask Image. Maps to a command-line argument: `--outBrain %s`.

> outMaskeda boolean or a pathlike object or string representing a file

>   Masked T1 Map Image. Maps to a command-line argument: `--outMasked %s`.

> outMasked2a boolean or a pathlike object or string representing a file

>   Masked T1-weighted Image. Maps to a command-line argument: `--outMasked2 %s`.

> outMasked3a boolean or a pathlike object or string representing a file

>   Masked Filter Image. Maps to a command-line argument: `--outMasked3 %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outBraina pathlike object or string representing an existing file

>   Brain Mask Image.

> outMaskeda pathlike object or string representing an existing file

>   Masked T1 Map Image.

> outMasked2a pathlike object or string representing an existing file

>   Masked T1-weighted Image.

> outMasked3a pathlike object or string representing an existing file

>   Masked Filter Image.

## JistBrainPartialVolumeFilter

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainPartialVolumeFilter`.

> Partial Volume Filter.

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

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inInputa pathlike object or string representing an existing file

>   Input Image. Maps to a command-line argument: `--inInput %s`.

> inPV‘bright’ or ‘dark’ or ‘both’

>   Outputs the raw intensity values or a probability score for the partial volume regions. Maps to a command-line argument: `--inPV %s`.

> inoutput‘probability’ or ‘intensity’

>   Output. Maps to a command-line argument: `--inoutput %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outPartiala boolean or a pathlike object or string representing a file

>   Partial Volume Image. Maps to a command-line argument: `--outPartial %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outPartiala pathlike object or string representing an existing file

>   Partial Volume Image.

## JistCortexSurfaceMeshInflation

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.cortex.JistCortexSurfaceMeshInflation`.

> Inflates a cortical surface mesh.

> References

> 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.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inLevelseta pathlike object or string representing an existing file

>   Levelset Image. Maps to a command-line argument: `--inLevelset %s`.

> inLorentzian‘true’ or ‘false’

>   Lorentzian Norm. Maps to a command-line argument: `--inLorentzian %s`.

> inMaxan integer

>   Max Iterations. Maps to a command-line argument: `--inMax %d`.

> inMeana float

>   Mean Curvature Threshold. Maps to a command-line argument: `--inMean %f`.

> inSORa float

>   SOR Parameter. Maps to a command-line argument: `--inSOR %f`.

> inStepan integer

>   Step Size. Maps to a command-line argument: `--inStep %d`.

> inTopology‘26/6’ or ‘6/26’ or ‘18/6’ or ‘6/18’ or ‘6/6’ or ‘wcs’ or ‘wco’ or ‘no’

>   Topology. Maps to a command-line argument: `--inTopology %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outInflateda boolean or a pathlike object or string representing a file

>   Inflated Surface. Maps to a command-line argument: `--outInflated %s`.

> outOriginala boolean or a pathlike object or string representing a file

>   Original Surface. Maps to a command-line argument: `--outOriginal %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outInflateda pathlike object or string representing an existing file

>   Inflated Surface.

> outOriginala pathlike object or string representing an existing file

>   Original Surface.

## JistIntensityMp2rageMasking

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.intensity.JistIntensityMp2rageMasking`.

> Estimate a background signal mask for a MP2RAGE dataset.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inBackground‘exponential’ or ‘half-normal’

>   Model distribution for background noise (default is half-normal, exponential is more stringent). Maps to a command-line argument: `--inBackground %s`.

> inMasking‘binary’ or ‘proba’

>   Whether to use a binary threshold or a weighted average based on the probability. Maps to a command-line argument: `--inMasking %s`.

> inQuantitativea pathlike object or string representing an existing file

>   Quantitative T1 Map (T1_Images) Image. Maps to a command-line argument: `--inQuantitative %s`.

> inSeconda pathlike object or string representing an existing file

>   Second inversion (Inv2) Image. Maps to a command-line argument: `--inSecond %s`.

> inSkip‘true’ or ‘false’

>   Skip zero values. Maps to a command-line argument: `--inSkip %s`.

> inT1weighteda pathlike object or string representing an existing file

>   T1-weighted (UNI) Image. Maps to a command-line argument: `--inT1weighted %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outMaskeda boolean or a pathlike object or string representing a file

>   Masked T1 Map Image. Maps to a command-line argument: `--outMasked_T1_Map %s`.

> outMasked2a boolean or a pathlike object or string representing a file

>   Masked Iso Image. Maps to a command-line argument: `--outMasked_T1weighted %s`.

> outSignala boolean or a pathlike object or string representing a file

>   Signal Proba Image. Maps to a command-line argument: `--outSignal_Proba %s`.

> outSignal2a boolean or a pathlike object or string representing a file

>   Signal Mask Image. Maps to a command-line argument: `--outSignal_Mask %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outMaskeda pathlike object or string representing an existing file

>   Masked T1 Map Image.

> outMasked2a pathlike object or string representing an existing file

>   Masked Iso Image.

> outSignala pathlike object or string representing an existing file

>   Signal Proba Image.

> outSignal2a pathlike object or string representing an existing file

>   Signal Mask Image.

## JistLaminarProfileCalculator

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarProfileCalculator`.

> Compute various moments for intensities mapped along a cortical profile.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inIntensitya pathlike object or string representing an existing file

>   Intensity Profile Image. Maps to a command-line argument: `--inIntensity %s`.

> inMaska pathlike object or string representing an existing file

>   Mask Image (opt, 3D or 4D). Maps to a command-line argument: `--inMask %s`.

> incomputed‘mean’ or ‘stdev’ or ‘skewness’ or ‘kurtosis’

>   Computed statistic. Maps to a command-line argument: `--incomputed %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outResulta boolean or a pathlike object or string representing a file

>   Result. Maps to a command-line argument: `--outResult %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outResulta pathlike object or string representing an existing file

>   Result.

## JistLaminarProfileGeometry

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarProfileGeometry`.

> Compute various geometric quantities for a cortical layers.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inProfilea pathlike object or string representing an existing file

>   Profile Surface Image. Maps to a command-line argument: `--inProfile %s`.

> incomputed‘thickness’ or ‘curvedness’ or ‘shape_index’ or ‘mean_curvature’ or ‘gauss_curvature’ or ‘profile_length’ or ‘profile_curvature’ or ‘profile_torsion’

>   Computed measure. Maps to a command-line argument: `--incomputed %s`.

> inoutsidea float

>   Outside extension (mm). Maps to a command-line argument: `--inoutside %f`.

> inregularization‘none’ or ‘Gaussian’

>   Regularization. Maps to a command-line argument: `--inregularization %s`.

> insmoothinga float

>   Smoothing parameter. Maps to a command-line argument: `--insmoothing %f`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outResulta boolean or a pathlike object or string representing a file

>   Result. Maps to a command-line argument: `--outResult %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outResulta pathlike object or string representing an existing file

>   Result.

## JistLaminarProfileSampling

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarProfileSampling`.

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

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inCortexa pathlike object or string representing an existing file

>   Cortex Mask (opt). Maps to a command-line argument: `--inCortex %s`.

> inIntensitya pathlike object or string representing an existing file

>   Intensity Image. Maps to a command-line argument: `--inIntensity %s`.

> inProfilea pathlike object or string representing an existing file

>   Profile Surface Image. Maps to a command-line argument: `--inProfile %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outProfile2a boolean or a pathlike object or string representing a file

>   Profile 4D Mask. Maps to a command-line argument: `--outProfile2 %s`.

> outProfilemappeda boolean or a pathlike object or string representing a file

>   Profile-mapped Intensity Image. Maps to a command-line argument: `--outProfilemapped %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outProfile2a pathlike object or string representing an existing file

>   Profile 4D Mask.

> outProfilemappeda pathlike object or string representing an existing file

>   Profile-mapped Intensity Image.

## JistLaminarROIAveraging

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarROIAveraging`.

> Compute an average profile over a given ROI.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inIntensitya pathlike object or string representing an existing file

>   Intensity Profile Image. Maps to a command-line argument: `--inIntensity %s`.

> inMaska pathlike object or string representing an existing file

>   Mask Image (opt, 3D or 4D). Maps to a command-line argument: `--inMask %s`.

> inROIa pathlike object or string representing an existing file

>   ROI Mask. Maps to a command-line argument: `--inROI %s`.

> inROI2a string

>   ROI Name. Maps to a command-line argument: `--inROI2 %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outROI3a boolean or a pathlike object or string representing a file

>   ROI Average. Maps to a command-line argument: `--outROI3 %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outROI3a pathlike object or string representing an existing file

>   ROI Average.

## JistLaminarVolumetricLayering

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarVolumetricLayering`.

> Volumetric Layering.

> Builds a continuous layering of the cortex following distance-preserving or volume-preserving models of cortical folding.

> References

> Waehnert MD, Dinse J, Weiss M, Streicher MN, Waehnert P, Geyer S, Turner R, Bazin PL, Anatomically motivated modeling of cortical laminae, Neuroimage, 2013.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inInnera pathlike object or string representing an existing file

>   Inner Distance Image (GM/WM boundary). Maps to a command-line argument: `--inInner %s`.

> inLayering‘distance-preserving’ or ‘volume-preserving’

>   Layering method. Maps to a command-line argument: `--inLayering %s`.

> inLayering2‘outward’ or ‘inward’

>   Layering direction. Maps to a command-line argument: `--inLayering2 %s`.

> inMaxan integer

>   Max iterations for narrow band evolution. Maps to a command-line argument: `--inMax %d`.

> inMina float

>   Min change ratio for narrow band evolution. Maps to a command-line argument: `--inMin %f`.

> inNumberan integer

>   Number of layers. Maps to a command-line argument: `--inNumber %d`.

> inOutera pathlike object or string representing an existing file

>   Outer Distance Image (CSF/GM boundary). Maps to a command-line argument: `--inOuter %s`.

> inTopology‘26/6’ or ‘6/26’ or ‘18/6’ or ‘6/18’ or ‘6/6’ or ‘wcs’ or ‘wco’ or ‘no’

>   Topology. Maps to a command-line argument: `--inTopology %s`.

> incurvaturean integer

>   Curvature approximation scale (voxels). Maps to a command-line argument: `--incurvature %d`.

> inpresmooth‘true’ or ‘false’

>   Pre-smooth cortical surfaces. Maps to a command-line argument: `--inpresmooth %s`.

> inratioa float

>   Ratio smoothing kernel size (voxels). Maps to a command-line argument: `--inratio %f`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outContinuousa boolean or a pathlike object or string representing a file

>   Continuous depth measurement. Maps to a command-line argument: `--outContinuous %s`.

> outDiscretea boolean or a pathlike object or string representing a file

>   Discrete sampled layers. Maps to a command-line argument: `--outDiscrete %s`.

> outLayera boolean or a pathlike object or string representing a file

>   Layer boundary surfaces. Maps to a command-line argument: `--outLayer %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outContinuousa pathlike object or string representing an existing file

>   Continuous depth measurement.

> outDiscretea pathlike object or string representing an existing file

>   Discrete sampled layers.

> outLayera pathlike object or string representing an existing file

>   Layer boundary surfaces.

## MedicAlgorithmImageCalculator

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculator`.

> Perform simple image calculator operations on two images.

> The operations include ‘Add’, ‘Subtract’, ‘Multiply’, and ‘Divide’

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inOperation‘Add’ or ‘Subtract’ or ‘Multiply’ or ‘Divide’ or ‘Min’ or ‘Max’

>   Operation. Maps to a command-line argument: `--inOperation %s`.

> inVolumea pathlike object or string representing an existing file

>   Volume 1. Maps to a command-line argument: `--inVolume %s`.

> inVolume2a pathlike object or string representing an existing file

>   Volume 2. Maps to a command-line argument: `--inVolume2 %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outResulta boolean or a pathlike object or string representing a file

>   Result Volume. Maps to a command-line argument: `--outResult %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outResulta pathlike object or string representing an existing file

>   Result Volume.

## MedicAlgorithmLesionToads

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmLesionToads`.

> Algorithm for simultaneous 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.

> References

> 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.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inAtlas‘With Lesion’ or ‘No Lesion’

>   Atlas to Use. Maps to a command-line argument: `--inAtlas %s`.

> inAtlas2a pathlike object or string representing an existing file

>   Atlas File - With Lesions. Maps to a command-line argument: `--inAtlas2 %s`.

> inAtlas3a pathlike object or string representing an existing file

>   Atlas File - No Lesion - T1 and FLAIR. Maps to a command-line argument: `--inAtlas3 %s`.

> inAtlas4a pathlike object or string representing an existing file

>   Atlas File - No Lesion - T1 Only. Maps to a command-line argument: `--inAtlas4 %s`.

> inAtlas5a float

>   Controls the effect of the statistical atlas on the segmentation. Maps to a command-line argument: `--inAtlas5 %f`.

> inAtlas6‘rigid’ or ‘multi_fully_affine’

>   Atlas alignment. Maps to a command-line argument: `--inAtlas6 %s`.

> inConnectivity‘(26,6)’ or ‘(6,26)’ or ‘(6,18)’ or ‘(18,6)’

>   Connectivity (foreground,background). Maps to a command-line argument: `--inConnectivity %s`.

> inCorrect‘true’ or ‘false’

>   Correct MR field inhomogeneity. Maps to a command-line argument: `--inCorrect %s`.

> inFLAIRa pathlike object or string representing an existing file

>   FLAIR Image. Maps to a command-line argument: `--inFLAIR %s`.

> inInclude‘true’ or ‘false’

>   Include lesion in WM class in hard classification. Maps to a command-line argument: `--inInclude %s`.

> inMaximuman integer

>   Maximum distance from the interventricular WM boundary to downweight the lesion membership to avoid false positives. Maps to a command-line argument: `--inMaximum %d`.

> inMaximum2an integer

>   Maximum Ventircle Distance. Maps to a command-line argument: `--inMaximum2 %d`.

> inMaximum3an integer

>   Maximum InterVentricular Distance. Maps to a command-line argument: `--inMaximum3 %d`.

> inMaximum4a float

>   Maximum amount of relative change in the energy function considered as the convergence criteria. Maps to a command-line argument: `--inMaximum4 %f`.

> inMaximum5an integer

>   Maximum iterations. Maps to a command-line argument: `--inMaximum5 %d`.

> inOutput‘hard segmentation’ or ‘hard segmentation+memberships’ or ‘cruise inputs’ or ‘dura removal inputs’

>   Output images. Maps to a command-line argument: `--inOutput %s`.

> inOutput2‘true’ or ‘false’

>   Output the hard classification using maximum membership (not neceesarily topologically correct). Maps to a command-line argument: `--inOutput2 %s`.

> inOutput3‘true’ or ‘false’

>   Output the estimated inhomogeneity field. Maps to a command-line argument: `--inOutput3 %s`.

> inSmootinga float

>   Controls the effect of neighborhood voxels on the membership. Maps to a command-line argument: `--inSmooting %f`.

> inT1_MPRAGEa pathlike object or string representing an existing file

>   T1_MPRAGE Image. Maps to a command-line argument: `--inT1_MPRAGE %s`.

> inT1_SPGRa pathlike object or string representing an existing file

>   T1_SPGR Image. Maps to a command-line argument: `--inT1_SPGR %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outCorticala boolean or a pathlike object or string representing a file

>   Cortical GM Membership. Maps to a command-line argument: `--outCortical %s`.

> outFilleda boolean or a pathlike object or string representing a file

>   Filled WM Membership. Maps to a command-line argument: `--outFilled %s`.

> outHarda boolean or a pathlike object or string representing a file

>   Hard segmentation. Maps to a command-line argument: `--outHard %s`.

> outHard2a boolean or a pathlike object or string representing a file

>   Hard segmentationfrom memberships. Maps to a command-line argument: `--outHard2 %s`.

> outInhomogeneitya boolean or a pathlike object or string representing a file

>   Inhomogeneity Field. Maps to a command-line argument: `--outInhomogeneity %s`.

> outLesiona boolean or a pathlike object or string representing a file

>   Lesion Segmentation. Maps to a command-line argument: `--outLesion %s`.

> outMembershipa boolean or a pathlike object or string representing a file

>   Membership Functions. Maps to a command-line argument: `--outMembership %s`.

> outSulcala boolean or a pathlike object or string representing a file

>   Sulcal CSF Membership. Maps to a command-line argument: `--outSulcal %s`.

> outWMa boolean or a pathlike object or string representing a file

>   WM Mask. Maps to a command-line argument: `--outWM %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outCorticala pathlike object or string representing an existing file

>   Cortical GM Membership.

> outFilleda pathlike object or string representing an existing file

>   Filled WM Membership.

> outHarda pathlike object or string representing an existing file

>   Hard segmentation.

> outHard2a pathlike object or string representing an existing file

>   Hard segmentationfrom memberships.

> outInhomogeneitya pathlike object or string representing an existing file

>   Inhomogeneity Field.

> outLesiona pathlike object or string representing an existing file

>   Lesion Segmentation.

> outMembershipa pathlike object or string representing an existing file

>   Membership Functions.

> outSulcala pathlike object or string representing an existing file

>   Sulcal CSF Membership.

> outWMa pathlike object or string representing an existing file

>   WM Mask.

## MedicAlgorithmMipavReorient

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient`.

> Reorient a volume to a particular anatomical orientation.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> 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. Maps to a command-line argument: `--inInterpolation %s`.

> inNew‘Dicom axial’ or ‘Dicom coronal’ or ‘Dicom sagittal’ or ‘User defined’

>   New image orientation. Maps to a command-line argument: `--inNew %s`.

> inResolution‘Unchanged’ or ‘Finest cubic’ or ‘Coarsest cubic’ or ‘Same as template’

>   Resolution. Maps to a command-line argument: `--inResolution %s`.

> inSourcea list of items which are a pathlike object or string representing a file

>   Source. Maps to a command-line argument: `--inSource %s`.

> inTemplatea pathlike object or string representing an existing file

>   Template. Maps to a command-line argument: `--inTemplate %s`.

> inUser‘Unknown’ or ‘Patient Right to Left’ or ‘Patient Left to Right’ or ‘Patient Posterior to Anterior’ or ‘Patient Anterior to Posterior’ or ‘Patient Inferior to Superior’ or ‘Patient Superior to Inferior’

>   User defined X-axis orientation (image left to right). Maps to a command-line argument: `--inUser %s`.

> inUser2‘Unknown’ or ‘Patient Right to Left’ or ‘Patient Left to Right’ or ‘Patient Posterior to Anterior’ or ‘Patient Anterior to Posterior’ or ‘Patient Inferior to Superior’ or ‘Patient Superior to Inferior’

>   User defined Y-axis orientation (image top to bottom). Maps to a command-line argument: `--inUser2 %s`.

> inUser3‘Unknown’ or ‘Patient Right to Left’ or ‘Patient Left to Right’ or ‘Patient Posterior to Anterior’ or ‘Patient Anterior to Posterior’ or ‘Patient Inferior to Superior’ or ‘Patient Superior to Inferior’

>   User defined Z-axis orientation (into the screen). Maps to a command-line argument: `--inUser3 %s`.

> inUser4‘Axial’ or ‘Coronal’ or ‘Sagittal’ or ‘Unknown’

>   User defined Image Orientation. Maps to a command-line argument: `--inUser4 %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outReorienteda list of items which are a pathlike object or string representing a file

>   Reoriented Volume. Maps to a command-line argument: `--outReoriented %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

## MedicAlgorithmN3

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmN3`.

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

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> 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. Maps to a command-line argument: `--inAutomatic %s`.

> inEnda 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. Maps to a command-line argument: `--inEnd %f`.

> inFielda 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. Maps to a command-line argument: `--inField %f`.

> inInputa pathlike object or string representing an existing file

>   Input Volume. Maps to a command-line argument: `--inInput %s`.

> inKernela 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. Maps to a command-line argument: `--inKernel %f`.

> inMaximuman integer

>   Maximum number of Iterations. Maps to a command-line argument: `--inMaximum %d`.

> inSignala float

>   Default = min + 1, Values at less than threshold are treated as part of the background. Maps to a command-line argument: `--inSignal %f`.

> inSubsamplea 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. Maps to a command-line argument: `--inSubsample %f`.

> inWeinera float

>   Usually between 0.0-1.0. Maps to a command-line argument: `--inWeiner %f`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outInhomogeneitya boolean or a pathlike object or string representing a file

>   Inhomogeneity Corrected Volume. Maps to a command-line argument: `--outInhomogeneity %s`.

> outInhomogeneity2a boolean or a pathlike object or string representing a file

>   Inhomogeneity Field. Maps to a command-line argument: `--outInhomogeneity2 %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outInhomogeneitya pathlike object or string representing an existing file

>   Inhomogeneity Corrected Volume.

> outInhomogeneity2a pathlike object or string representing an existing file

>   Inhomogeneity Field.

## MedicAlgorithmSPECTRE2010

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010`.

> SPECTRE 2010: Simple Paradigm for Extra-Cranial Tissue REmoval [1], [2].

> References

> [1]

> 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.

> [2]

> 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.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inApply‘All’ or ‘X’ or ‘Y’ or ‘Z’

>   Apply rotation. Maps to a command-line argument: `--inApply %s`.

> inAtlasa pathlike object or string representing an existing file

>   SPECTRE atlas description file. A text file enumerating atlas files and landmarks. Maps to a command-line argument: `--inAtlas %s`.

> inBackgrounda float

>   Maps to a command-line argument: `--inBackground %f`.

> inCoarsea float

>   Coarse angle increment. Maps to a command-line argument: `--inCoarse %f`.

> inCost‘Correlation ratio’ or ‘Least squares’ or ‘Normalized cross correlation’ or ‘Normalized mutual information’

>   Cost function. Maps to a command-line argument: `--inCost %s`.

> inDegrees‘Rigid - 6’ or ‘Global rescale - 7’ or ‘Specific rescale - 9’ or ‘Affine - 12’

>   Degrees of freedom. Maps to a command-line argument: `--inDegrees %s`.

> inFind‘true’ or ‘false’

>   Find Midsaggital Plane. Maps to a command-line argument: `--inFind %s`.

> inFinea float

>   Fine angle increment. Maps to a command-line argument: `--inFine %f`.

> inImage‘T1_SPGR’ or ‘T1_ALT’ or ‘T1_MPRAGE’ or ‘T2’ or ‘FLAIR’

>   Set the image modality. MP-RAGE is recommended for most T1 sequence images. Maps to a command-line argument: `--inImage %s`.

> inInhomogeneity‘true’ or ‘false’

>   Set to false by default, this parameter will make FANTASM try to do inhomogeneity correction during it’s iterative cycle. Maps to a command-line argument: `--inInhomogeneity %s`.

> inInitialan integer

>   Erosion of the initial mask, which is based on the probability mask and the classification., The initial mask is output as the d0 volume at the conclusion of SPECTRE. Maps to a command-line argument: `--inInitial %d`.

> inInitial2a float

>   Initial probability threshold. Maps to a command-line argument: `--inInitial2 %f`.

> inInputa pathlike object or string representing an existing file

>   Input volume to be skullstripped. Maps to a command-line argument: `--inInput %s`.

> inMMCan integer

>   The size of the dilation step within the Modified Morphological Closing. Maps to a command-line argument: `--inMMC %d`.

> inMMC2an integer

>   The size of the erosion step within the Modified Morphological Closing. Maps to a command-line argument: `--inMMC2 %d`.

> inMaximuma float

>   Maximum angle. Maps to a command-line argument: `--inMaximum %f`.

> inMinimuma float

>   Minimum probability threshold. Maps to a command-line argument: `--inMinimum %f`.

> inMinimum2a float

>   Minimum angle. Maps to a command-line argument: `--inMinimum2 %f`.

> inMultiplean integer

>   Multiple of tolerance to bracket the minimum. Maps to a command-line argument: `--inMultiple %d`.

> inMultithreading‘true’ or ‘false’

>   Set to false by default, this parameter controls the multithreaded behavior of the linear registration. Maps to a command-line argument: `--inMultithreading %s`.

> inNumberan integer

>   Number of iterations. Maps to a command-line argument: `--inNumber %d`.

> inNumber2an integer

>   Number of minima from Level 8 to test at Level 4. Maps to a command-line argument: `--inNumber2 %d`.

> inOutput‘true’ or ‘false’

>   Determines if the output results are transformed back into the space of the original input image. Maps to a command-line argument: `--inOutput %s`.

> inOutput2‘true’ or ‘false’

>   Output Plane?. Maps to a command-line argument: `--inOutput2 %s`.

> inOutput3‘true’ or ‘false’

>   Output Split-Halves?. Maps to a command-line argument: `--inOutput3 %s`.

> inOutput4‘true’ or ‘false’

>   Output Segmentation on Plane?. Maps to a command-line argument: `--inOutput4 %s`.

> inOutput5‘Trilinear’ or ‘Bspline 3rd order’ or ‘Bspline 4th order’ or ‘Cubic Lagrangian’ or ‘Quintic Lagrangian’ or ‘Heptic Lagrangian’ or ‘Windowed sinc’ or ‘Nearest Neighbor’

>   Output interpolation. Maps to a command-line argument: `--inOutput5 %s`.

> inRegistration‘Trilinear’ or ‘Bspline 3rd order’ or ‘Bspline 4th order’ or ‘Cubic Lagrangian’ or ‘Quintic Lagrangian’ or ‘Heptic Lagrangian’ or ‘Windowed sinc’

>   Registration interpolation. Maps to a command-line argument: `--inRegistration %s`.

> inResample‘true’ or ‘false’

>   Determines if the data is resampled to be isotropic during the processing. Maps to a command-line argument: `--inResample %s`.

> inRun‘true’ or ‘false’

>   Run Smooth Brain Mask. Maps to a command-line argument: `--inRun %s`.

> inSkip‘true’ or ‘false’

>   Skip multilevel search (Assume images are close to alignment). Maps to a command-line argument: `--inSkip %s`.

> inSmoothinga float

>   Maps to a command-line argument: `--inSmoothing %f`.

> inSubsample‘true’ or ‘false’

>   Subsample image for speed. Maps to a command-line argument: `--inSubsample %s`.

> inUse‘true’ or ‘false’

>   Use the max of the min resolutions of the two datasets when resampling. Maps to a command-line argument: `--inUse %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outFANTASMa boolean or a pathlike object or string representing a file

>   Tissue classification of the whole input volume. Maps to a command-line argument: `--outFANTASM %s`.

> outMaska boolean or a pathlike object or string representing a file

>   Binary Mask of the skullstripped result with just the brain. Maps to a command-line argument: `--outMask %s`.

> outMidsagittala boolean or a pathlike object or string representing a file

>   Plane dividing the brain hemispheres. Maps to a command-line argument: `--outMidsagittal %s`.

> outOriginala boolean or a pathlike object or string representing a file

>   If Output in Original Space Flag is true then outputs the original input volume. Otherwise outputs the axialy reoriented input volume. Maps to a command-line argument: `--outOriginal %s`.

> outPriora boolean or a pathlike object or string representing a file

>   Probability prior from the atlas registrations. Maps to a command-line argument: `--outPrior %s`.

> outSegmentationa boolean or a pathlike object or string representing a file

>   2D image showing the tissue classification on the midsagittal plane. Maps to a command-line argument: `--outSegmentation %s`.

> outSplitHalvesa boolean or a pathlike object or string representing a file

>   Skullstripped mask of the brain with the hemispheres divided. Maps to a command-line argument: `--outSplitHalves %s`.

> outStrippeda boolean or a pathlike object or string representing a file

>   Skullstripped result of the input volume with just the brain. Maps to a command-line argument: `--outStripped %s`.

> outd0a boolean or a pathlike object or string representing a file

>   Initial Brainmask. Maps to a command-line argument: `--outd0 %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outFANTASMa pathlike object or string representing an existing file

>   Tissue classification of the whole input volume.

> outMaska pathlike object or string representing an existing file

>   Binary Mask of the skullstripped result with just the brain.

> outMidsagittala pathlike object or string representing an existing file

>   Plane dividing the brain hemispheres.

> outOriginala pathlike object or string representing an existing file

>   If Output in Original Space Flag is true then outputs the original input volume. Otherwise outputs the axialy reoriented input volume.

> outPriora pathlike object or string representing an existing file

>   Probability prior from the atlas registrations.

> outSegmentationa pathlike object or string representing an existing file

>   2D image showing the tissue classification on the midsagittal plane.

> outSplitHalvesa pathlike object or string representing an existing file

>   Skullstripped mask of the brain with the hemispheres divided.

> outStrippeda pathlike object or string representing an existing file

>   Skullstripped result of the input volume with just the brain.

> outd0a pathlike object or string representing an existing file

>   Initial Brainmask.

## MedicAlgorithmThresholdToBinaryMask

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThresholdToBinaryMask`.

> Threshold to Binary Mask.

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

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inLabela list of items which are a pathlike object or string representing a file

>   Input volumes. Maps to a command-line argument: `--inLabel %s`.

> inMaximuma float

>   Maximum threshold value. Maps to a command-line argument: `--inMaximum %f`.

> inMinimuma float

>   Minimum threshold value. Maps to a command-line argument: `--inMinimum %f`.

> inUse‘true’ or ‘false’

>   Use the images max intensity as the max value of the range. Maps to a command-line argument: `--inUse %s`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outBinarya list of items which are a pathlike object or string representing a file

>   Binary Mask. Maps to a command-line argument: `--outBinary %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

## RandomVol

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `java edu.jhu.ece.iacl.jist.cli.run edu.jhu.bme.smile.demo.RandomVol`.

> Generate a volume of random scalars.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inField‘Uniform’ or ‘Normal’ or ‘Exponential’

>   Field. Maps to a command-line argument: `--inField %s`.

> inLambdaa float

>   Lambda Value for Exponential Distribution. Maps to a command-line argument: `--inLambda %f`.

> inMaximuman integer

>   Maximum Value. Maps to a command-line argument: `--inMaximum %d`.

> inMinimuman integer

>   Minimum Value. Maps to a command-line argument: `--inMinimum %d`.

> inSizean integer

>   Size of Volume in X direction. Maps to a command-line argument: `--inSize %d`.

> inSize2an integer

>   Size of Volume in Y direction. Maps to a command-line argument: `--inSize2 %d`.

> inSize3an integer

>   Size of Volume in Z direction. Maps to a command-line argument: `--inSize3 %d`.

> inSize4an integer

>   Size of Volume in t direction. Maps to a command-line argument: `--inSize4 %d`.

> inStandardan integer

>   Standard Deviation for Normal Distribution. Maps to a command-line argument: `--inStandard %d`.

> nulla string

>   Execution Time. Maps to a command-line argument: `--null %s`.

> outRand1a boolean or a pathlike object or string representing a file

>   Rand1. Maps to a command-line argument: `--outRand1 %s`.

> xDefaultMeman integer

>   Set default maximum heap size. Maps to a command-line argument: `-xDefaultMem %d`.

> xMaxProcessan integer

>   Set default maximum number of processes. Maps to a command-line argument: `-xMaxProcess %d`. (Nipype default value: `1`)

> xPrefExt‘nrrd’

>   Output File Type. Maps to a command-line argument: `--xPrefExt %s`.

> outRand1a pathlike object or string representing an existing file

>   Rand1.