nipype.interfaces.mipav.developer module¶
Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.
JistBrainMgdmSegmentation¶
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¶
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¶
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¶
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¶
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¶
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¶
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¶
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¶
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¶
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¶
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¶
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¶
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¶
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¶
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¶
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
- 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 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 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¶
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¶
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.