3 Yd@sdZddlZddlmZmZmZmZmZmZm Z m Z m Z m Z GdddeZ GdddeZGd d d eZGd d d eZGd ddeZGdddeZGdddeZGdddeZGdddeZGdddeZGdddeZGdddeZGdddeZGdd d eZGd!d"d"eZGd#d$d$eZGd%d&d&eZGd'd(d(eZGd)d*d*eZGd+d,d,eZ Gd-d.d.eZ!Gd/d0d0eZ"Gd1d2d2eZ#Gd3d4d4eZ$Gd5d6d6eZ%Gd7d8d8eZ&Gd9d:d:eZ'Gd;d<dd>eZ)Gd?d@d@eZ*GdAdBdBeZ+GdCdDdDeZ,GdEdFdFeZ-GdGdHdHeZ.GdIdJdJeZ/GdKdLdLeZ0GdMdNdNeZ1GdOdPdPeZ2GdQdRdReZ3GdSdTdTeZ4GdUdVdVeZ5GdWdXdXeZ6GdYdZdZeZ7Gd[d\d\eZ8Gd]d^d^eZ9Gd_d`d`eZ:GdadbdbeZ;GdcddddeZGdidjdjeZ?GdkdldleZ@GdmdndneZAGdodpdpeZBdS)qzuAutogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.N) CommandLineCommandLineInputSpecSEMLikeCommandLine TraitedSpecFile Directorytraits isdefinedInputMultiPathOutputMultiPathc @sHeZdZeddddZeddddZejddd Zejd d d Z ej d d d Z ej ddddd Z ej ddddd Zejddd Zej ddd Zej ddddd Zej ddd d!d"d#d$d%d&d'd Zej d(d)d*d Zejejed+d,d-d.Zejejed+d/d0d.Zejejed+d1d2d.Zejd3d4d Zejd5d6d Zejd7d8d9dd:Zd;S)<&JistLaminarVolumetricLayeringInputSpecz%Inner Distance Image (GM/WM boundary)Tz --inInner %s)descexistsargstrz&Outer Distance Image (CSF/GM boundary)z --inOuter %szNumber of layersz --inNumber %d)rrz(Max iterations for narrow band evolutionz --inMax %dz*Min change ratio for narrow band evolutionz --inMin %fzdistance-preservingzvolume-preservingzLayering methodz--inLayering %sZoutwardZinwardzLayering directionz--inLayering2 %sz&curvature approximation scale (voxels)z--incurvature %dz$ratio smoothing kernel size (voxels)z --inratio %ftruefalsezpre-smooth cortical surfacesz--inpresmooth %sz26/6z6/26z18/6z6/18z6/6wcswconoTopologyz--inTopology %snrrdzOutput File Typez --xPrefExt %sFzContinuous depth measurementz--outContinuous %s) hash_filesrrzDiscrete sampled layersz--outDiscrete %szLayer boundary surfacesz --outLayer %szExecution Timez --null %szSet default maximum heap sizez-xDefaultMem %dz(Set default maximum number of processes.z-xMaxProcess %d)rr usedefaultN)__name__ __module__ __qualname__rZinInnerZinOuterr IntinNumberinMaxFloatinMinEnumZ inLayeringZ inLayering2Z incurvatureZinratioZ inpresmooth inTopologyxPrefExtEitherBool outContinuous outDiscreteoutLayerStrnull xDefaultMem xMaxProcessr/r/S/var/www/html/virt/lib/python3.6/site-packages/nipype/interfaces/mipav/developer.pyr s|      r c@s0eZdZedddZedddZedddZdS)'JistLaminarVolumetricLayeringOutputSpeczContinuous depth measurementT)rrzDiscrete sampled layerszLayer boundary surfacesN)rrrrr(r)r*r/r/r/r0r1fs  r1c@s,eZdZdZeZeZdZddddZ dZ dS) JistLaminarVolumetricLayeringaaVolumetric Layering. Builds a continuous layering of the cortex following distance-preserving or volume-preserving models of cortical folding. References ---------- Waehnert MD, Dinse J, Weiss M, Streicher MN, Waehnert P, Geyer S, Turner R, Bazin PL, Anatomically motivated modeling of cortical laminae, Neuroimage, 2013. zYjava edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarVolumetricLayering zoutContinuous.niiz outLayer.niizoutDiscrete.nii)r(r*r)TN) rrr__doc__r input_specr1 output_spec_cmd_outputs_filenames _redirect_xr/r/r/r0r2ls r2c @seZdZeddddZeddddZeddddZed dd dZed dd dZed dddZ e j dddZ e j dddZ e j dddZe jdddZe j dddZe jdddZe jddddd d!d"d#d$d%d Ze jd&d'd(d)dZe jd&d'd*d+dZe jd,d-d.d/dZe jd0d1d2dZe je jed3d4d5d6Ze je jed3d7d8d6Ze je jed3d9d:d6Ze je jed3d;ddZ e jd?d@dZ!e jdAdBdCddDZ"dES)F"JistBrainMgdmSegmentationInputSpeczMP2RAGE T1 Map ImageTz--inMP2RAGE %s)rrrzMP2RAGE T1-weighted Imagez--inMP2RAGE2 %szPV / Dura Imagez --inPV %szMPRAGE T1-weighted Imagez --inMPRAGE %sz FLAIR Imagez --inFLAIR %sz Atlas filez --inAtlas %sz Data weightz --inData %f)rrzCurvature weightz--inCurvature %fzPosterior scale (mm)z--inPosterior %fzMax iterationsz --inMax %dz Min changez --inMin %fZStepsz --inSteps %dz26/6z6/26z18/6z6/18z6/6rrrrz--inTopology %srrzCompute posteriorsz--inCompute %szAdjust intensity priorsz --inAdjust %sZ segmentationZ membershipsz Output imagesz --inOutput %srzOutput File Typez --xPrefExt %sFzSegmented Brain Imagez--outSegmented %s)rrrzLevelset Boundary Imagez--outLevelset %sz"Posterior Maximum Memberships (4D)z--outPosterior2 %szPosterior Maximum Labels (4D)z--outPosterior3 %szExecution Timez --null %szSet default maximum heap sizez-xDefaultMem %drz(Set default maximum number of processes.z-xMaxProcess %d)rrrN)#rrrrZ inMP2RAGEZ inMP2RAGE2inPVZinMPRAGEinFLAIRinAtlasr r!ZinDataZ inCurvatureZ inPosteriorrr r"ZinStepsr#r$Z inComputeZinAdjustinOutputr%r&r' outSegmented outLevelset outPosterior2 outPosterior3r+r,r-r.r/r/r/r0r9s   r9c@s<eZdZedddZedddZedddZedddZdS)#JistBrainMgdmSegmentationOutputSpeczSegmented Brain ImageT)rrzLevelset Boundary Imagez"Posterior Maximum Memberships (4D)zPosterior Maximum Labels (4D)N)rrrrr>r?r@rAr/r/r/r0rBs   rBc@s.eZdZdZeZeZdZdddddZ dZ d S) JistBrainMgdmSegmentationzMGDM Whole Brain Segmentation. Estimate brain structures from an atlas for a MRI dataset (multiple input combinations are possible). zSjava edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainMgdmSegmentation zoutSegmented.niizoutPosterior2.niizoutPosterior3.niizoutLevelset.nii)r>r@rAr?TN) rrrr3r9r4rBr5r6r7r8r/r/r/r0rCsrCc @seZdZeddddZejddddd d d d d dd ZejdddddZej dddZ ej dddZ ejddddZ ej ejeddddZejdd dZejd!d"dZejd#d$d%dd&Zd'S)(#JistLaminarProfileGeometryInputSpeczProfile Surface ImageTz--inProfile %s)rrrZ thicknessZ curvednessZ shape_indexZmean_curvatureZgauss_curvatureZprofile_lengthZprofile_curvatureZprofile_torsionzcomputed measurez--incomputed %s)rrnoneZGaussianZregularizationz--inregularization %szsmoothing parameterz--insmoothing %fzoutside extension (mm)z--inoutside %frzOutput File Typez --xPrefExt %sFResultz--outResult %s)rrrzExecution Timez --null %szSet default maximum heap sizez-xDefaultMem %drz(Set default maximum number of processes.z-xMaxProcess %d)rrrN)rrrr inProfiler r# incomputedZinregularizationr!Z insmoothingZ inoutsider%r&r' outResultr+r,rr-r.r/r/r/r0rDs6 rDc@seZdZedddZdS)$JistLaminarProfileGeometryOutputSpecrFT)rrN)rrrrrIr/r/r/r0rJsrJc@s(eZdZdZeZeZdZddiZ dZ dS)JistLaminarProfileGeometryz;Compute various geometric quantities for a cortical layers.zVjava edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarProfileGeometry rIz outResult.niiTN) rrrr3rDr4rJr5r6r7r8r/r/r/r0rKs rKc@seZdZeddddZeddddZejddd d d d d Zejdddd Z ej ej eddddZ ej ddd Zejddd ZejdddddZdS)%JistLaminarProfileCalculatorInputSpeczIntensity Profile ImageTz--inIntensity %s)rrrzMask Image (opt, 3D or 4D)z --inMask %sZmeanZstdevZskewnessZkurtosiszcomputed statisticz--incomputed %s)rrrzOutput File Typez --xPrefExt %sFrFz--outResult %s)rrrzExecution Timez --null %szSet default maximum heap sizez-xDefaultMem %drz(Set default maximum number of processes.z-xMaxProcess %d)rrrN)rrrr inIntensityinMaskr r#rHr%r&r'rIr+r,rr-r.r/r/r/r0rLs*  rLc@seZdZedddZdS)&JistLaminarProfileCalculatorOutputSpecrFT)rrN)rrrrrIr/r/r/r0rO<srOc@s(eZdZdZeZeZdZddiZ dZ dS)JistLaminarProfileCalculatorzHCompute various moments for intensities mapped along a cortical profile.zXjava edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarProfileCalculator rIz outResult.niiTN) rrrr3rLr4rOr5r6r7r8r/r/r/r0rP@s rPc@seZdZeddddZejdddZejdd dZ ejd d dZ ejd d dZ ejdddZ ejdddZ ejdddZejdddddZejddddZejejeddddZejejeddd dZejd!d"dZejd#d$dZejd%d&d'dd(Zd)S)*MedicAlgorithmN3InputSpecz Input VolumeTz --inInput %s)rrrzVDefault = min + 1, Values at less than threshold are treated as part of the backgroundz --inSignal %f)rrzMaximum number of Iterationsz--inMaximum %dzUsually 0.01-0.00001, The measure used to terminate the iterations is the coefficient of variation of change in field estimates between successive iterations.z --inEnd %faCharacteristic 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.z --inField %fzUsually 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.z--inSubsample %fzUsually 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.z --inKernel %fzUsually between 0.0-1.0z --inWeiner %frrzxIf true determines the threshold by histogram analysis. If true a VOI cannot be used and the input threshold is ignored.z--inAutomatic %srzOutput File Typez --xPrefExt %sFzInhomogeneity Corrected Volumez--outInhomogeneity %s)rrrzInhomogeneity Fieldz--outInhomogeneity2 %szExecution Timez --null %szSet default maximum heap sizez-xDefaultMem %drz(Set default maximum number of processes.z-xMaxProcess %d)rrrN)rrrrinInputr r!ZinSignalr inMaximumZinEndinField inSubsampleZinKernelZinWeinerr#Z inAutomaticr%r&r'outInhomogeneityoutInhomogeneity2r+r,r-r.r/r/r/r0rQJsX rQc@s$eZdZedddZedddZdS)MedicAlgorithmN3OutputSpeczInhomogeneity Corrected VolumeT)rrzInhomogeneity FieldN)rrrrrVrWr/r/r/r0rXs rXc@s*eZdZdZeZeZdZdddZ dZ dS)MedicAlgorithmN3zPNon-parametric Intensity Non-uniformity Correction, N3, originally by J.G. Sled.z\java edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmN3 zoutInhomogeneity2.niizoutInhomogeneity.nii)rWrVTN) rrrr3rQr4rXr5r6r7r8r/r/r/r0rYsrYc@seZdZeddddZeddddZejddd Zed dd dZ ej d d dd Z ej ej eddddZejddd Zejddd ZejdddddZdS) JistLaminarROIAveragingInputSpeczIntensity Profile ImageTz--inIntensity %s)rrrzROI Maskz --inROI %szROI Namez --inROI2 %s)rrzMask Image (opt, 3D or 4D)z --inMask %srzOutput File Typez --xPrefExt %sFz ROI Averagez --outROI3 %s)rrrzExecution Timez --null %szSet default maximum heap sizez-xDefaultMem %drz(Set default maximum number of processes.z-xMaxProcess %d)rrrN)rrrrrMZinROIr r+ZinROI2rNr#r%r&r'outROI3r,rr-r.r/r/r/r0rZs   rZc@seZdZedddZdS)!JistLaminarROIAveragingOutputSpecz ROI AverageT)rrN)rrrrr[r/r/r/r0r\sr\c@s(eZdZdZeZeZdZddiZ dZ dS)JistLaminarROIAveragingz,Compute an average profile over a given ROI.zSjava edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.laminar.JistLaminarROIAveraging r[TN) rrrr3rZr4r\r5r6r7r8r/r/r/r0r]s r]c@speZdZeddddZeddddZeddddZejd d d d d Z ejddddddd Z ejddddd Z ejddddd Z ejddddd Z eddddZeddddZed dd!dZejd"d#d Zejd$d%d Zejd&d'd Zejddd(d)d Zejd*d+d Zejd,d-d Zejd.d/d Zejd0d1d Zejd2d3d4d5d Zejd6d7d8d9d:d;d Zejdd Zejejed?d@dAdBZ ejejed?dCdDdBZ!ejejed?dEdFdBZ"ejejed?dGdHdBZ#ejejed?dIdJdBZ$ejejed?dKdLdBZ%ejejed?dMdNdBZ&ejejed?dOdPdBZ'ejejed?dQdRdBZ(ej)dSdTd Z*ejdUdVd Z+ejdWdXdYddZZ,d[S)\"MedicAlgorithmLesionToadsInputSpeczT1_MPRAGE ImageTz--inT1_MPRAGE %s)rrrz T1_SPGR Imagez--inT1_SPGR %sz FLAIR Imagez --inFLAIR %sz With Lesionz No Lesionz Atlas to Usez --inAtlas %s)rrzhard segmentationzhard segmentation+membershipsz cruise inputszdura removal inputsz Output imagesz --inOutput %srrz_Output the hard classification using maximum membership (not neceesarily topologically correct)z--inOutput2 %szCorrect MR field inhomogeneity.z--inCorrect %sz(Output the estimated inhomogeneity fieldz--inOutput3 %szAtlas File - With Lesionsz --inAtlas2 %sz%Atlas File - No Lesion - T1 and FLAIRz --inAtlas3 %sz Atlas File - No Lesion - T1 Onlyz --inAtlas4 %szrMaximum distance from the interventricular WM boundary to downweight the lesion membership to avoid false postivesz--inMaximum %dzMaximum Ventircle Distancez--inMaximum2 %dz!Maximum InterVentricular Distancez--inMaximum3 %dz1Include lesion in WM class in hard classificationz--inInclude %sz@Controls the effect of the statistical atlas on the segmentationz --inAtlas5 %fzZd?S)@$MedicAlgorithmMipavReorientInputSpecZSource;z --inSource %s)rseprTemplateTz--inTemplate %s)rrrz Dicom axialz Dicom coronalzDicom sagittalz User definedzNew image orientationz --inNew %s)rrUnknownzPatient Right to LeftzPatient Left to RightzPatient Posterior to AnteriorzPatient Anterior to PosteriorzPatient Inferior to SuperiorzPatient Superior to Inferiorz5User defined X-axis orientation (image left to right)z --inUser %sz5User defined Y-axis orientation (image top to bottom)z --inUser2 %sz1User defined Z-axis orientation (into the screen)z --inUser3 %sZAxialZCoronalZSagittalzUser defined Image Orientationz --inUser4 %szNearest Neighbor TrilinearzBspline 3rd orderzBspline 4th orderzCubic LagrangianzQuintic LagrangianzHeptic Lagrangianz Windowed Sinc Interpolationz--inInterpolation %sZ Unchangedz Finest cubiczCoarsest cubiczSame as template Resolutionz--inResolution %srzOutput File Typez --xPrefExt %szReoriented Volumez--outReoriented %szExecution Timez --null %szSet default maximum heap sizez-xDefaultMem %drz(Set default maximum number of processes.z-xMaxProcess %d)rrrN)rrrr rZinSourceZ inTemplater r#ZinNewZinUserZinUser2ZinUser3ZinUser4ZinInterpolationZ inResolutionr%Z outReorientedr+r,rr-r.r/r/r/r0rs rc@s eZdZdS)%MedicAlgorithmMipavReorientOutputSpecN)rrrr/r/r/r0r(src@s$eZdZdZeZeZdZiZ dZ dS)MedicAlgorithmMipavReorientz9Reorient a volume to a particular anatomical orientation.zijava edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient TN) rrrr3rr4rr5r6r7r8r/r/r/r0r,s rc @sjeZdZeddddZeddddZejddd Zej d d d d dddd Z ej ddddd Z ej ddddd Z ej ddddd Z ej ddddd Zejddd Zejddd Zejdd d Zejd!d"d Zej ddd#d$d Zejd%d&Zejd'd&Zej ddd(d)d Zej ddd*d+d Zej ddd,d-d Zej d.d/d0d1d2d3d Zej d4d5d6d7d8d9d Zej d:d;dd?d@dAdBd Zej d:d;dd?d@dCdDdEd Zej dFdGdHdIdJdKd ZejdLdMd ZejdNdOd Z ejdPdQd Z!ejdRdSd Z"ejdTdUd Z#ejdVdWd Z$ejdXdYd Z%ej dddZd[d Z&ej ddd\d]d Z'ej ddd^d_d Z(ej ddd`dad Z)ej dbdcddd Z*ej+ej,ededfdgdhZ-ej+ej,ededidjdhZ.ej+ej,ededkdldhZ/ej+ej,ededmdndhZ0ej+ej,ededodpdhZ1ej+ej,ededqdrdhZ2ej+ej,ededsdtdhZ3ej+ej,ededudvdhZ4ej+ej,ededwdxdhZ5ej6dydzd Z7ejd{d|d Z8ejd}d~dddZ9dS)"MedicAlgorithmSPECTRE2010InputSpecz!Input volume to be skullstripped.Tz --inInput %s)rrrzRSPECTRE atlas description file. A text file enumerating atlas files and landmarks.z --inAtlas %szErosion of the inital mask, which is based on the probability mask and the classification., The initial mask is ouput as the d0 volume at the conclusion of SPECTRE.z--inInitial %d)rrZT1_SPGRZT1_ALTZ T1_MPRAGEZT2ZFLAIRzKSet the image modality. MP-RAGE is recommended for most T1 sequence images.z --inImage %srrzaDetermines if the output results are transformed back into the space of the original input image.z --inOutput %szFind Midsaggital Planez --inFind %szRun Smooth Brain Maskz --inRun %szJDetermines if the data is resampled to be isotropic during the processing.z--inResample %szInitial probability thresholdz--inInitial2 %fzMinimum probability thresholdz--inMinimum %fzHThe size of the dilation step within the Modified Morphological Closing.z --inMMC %dzGThe size of the erosion step within the Modified Morphological Closing.z --inMMC2 %dzySet to false by default, this parameter will make FANTASM try to do inhomogeneity correction during it's iterative cycle.z--inInhomogeneity %sz--inSmoothing %f)rz--inBackground %fz Output Plane?z--inOutput2 %szOutput Split-Halves?z--inOutput3 %szOutput Segmentation on Plane?z--inOutput4 %sz Rigid - 6zGlobal rescale - 7zSpecific rescale - 9z Affine - 12zDegrees of freedomz--inDegrees %szCorrelation ratioz Least squareszNormalized cross correlationzNormalized mutual informationz Cost functionz --inCost %srzBspline 3rd orderzBspline 4th orderzCubic LagrangianzQuintic LagrangianzHeptic Lagrangianz Windowed sinczRegistration interpolationz--inRegistration %szNearest NeighborzOutput interpolationz--inOutput5 %sZAllXYZzApply rotationz --inApply %sz Minimum anglez--inMinimum2 %fz Maximum anglez--inMaximum %fzCoarse angle incrementz --inCoarse %fzFine angle incrementz --inFine %fz,Multiple of tolerance to bracket the minimumz--inMultiple %dzNumber of iterationsz --inNumber %dz0Number of minima from Level 8 to test at Level 4z--inNumber2 %dzFUse the max of the min resolutions of the two datasets when resamplingz --inUse %szSubsample image for speedz--inSubsample %sz=Skip multilevel search (Assume images are close to alignment)z --inSkip %szgSet to false by default, this parameter controls the multithreaded behavior of the linear registration.z--inMultithreading %srzOutput File Typez --xPrefExt %sFzIf Output in Original Space Flag is true then outputs the original input volume. Otherwise outputs the axialy reoriented input volume.z--outOriginal %s)rrrz=Skullstripped result of the input volume with just the brain.z--outStripped %sz;Binary Mask of the skullstripped result with just the brainz --outMask %sz.Probability prior from the atlas registrationsz --outPrior %sz3Tissue classification of of the whole input volume.z--outFANTASM %szInitial Brainmaskz --outd0 %sz$Plane dividing the brain hemispheresz--outMidsagittal %sz=Skullstripped mask of the brain with the hemispheres divided.z--outSplitHalves %szC2D image showing the tissue classification on the midsagittal planez--outSegmentation %szExecution Timez --null %szSet default maximum heap sizez-xDefaultMem %drz(Set default maximum number of processes.z-xMaxProcess %d)rrrN):rrrrrRr<r rZ inInitialr#ZinImager=ZinFindZinRunZ inResampler!Z inInitial2r|ZinMMCZinMMC2ZinInhomogeneityZ inSmoothing inBackgroundr_r`Z inOutput4Z inDegreesZinCostZinRegistrationZ inOutput5ZinApplyZ inMinimum2rSZinCoarseZinFineZ inMultiplerZ inNumber2inUserUrnZinMultithreadingr%r&r'rv outStrippedoutMaskoutPrior outFANTASMoutd0outMidsagittaloutSplitHalvesoutSegmentationr+r,r-r.r/r/r/r0r6sh        rc@sxeZdZedddZedddZedddZedddZedddZedddZ ed ddZ ed ddZ ed ddZ d S) #MedicAlgorithmSPECTRE2010OutputSpeczIf Output in Original Space Flag is true then outputs the original input volume. Otherwise outputs the axialy reoriented input volume.T)rrz=Skullstripped result of the input volume with just the brain.z;Binary Mask of the skullstripped result with just the brainz.Probability prior from the atlas registrationsz3Tissue classification of of the whole input volume.zInitial Brainmaskz$Plane dividing the brain hemispheresz=Skullstripped mask of the brain with the hemispheres divided.zC2D image showing the tissue classification on the midsagittal planeN) rrrrrvrrrrrrrrr/r/r/r0rs&     rc @s8eZdZdZeZeZdZddddddd d d d Z d Z dS)MedicAlgorithmSPECTRE2010aSPECTRE 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. zojava edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010 z outd0.niizoutOriginal.niiz outMask.niizoutSplitHalves.niizoutMidsagittal.niiz outPrior.niizoutFANTASM.niizoutSegmentation.niizoutStripped.nii) rrvrrrrrrrTN) rrrr3rr4rr5r6r7r8r/r/r/r0r/src@seZdZeddddZejddddd d Zejd d d dd Zejdddd Z ej ej eddddZ ej ddd Zejddd ZejdddddZdS)%JistBrainPartialVolumeFilterInputSpecz Input ImageTz --inInput %s)rrrZbrightZdarkZbothzWOutputs the raw intensity values or a probability score for the partial volume regions.z --inPV %s)rrZ probabilityZ intensityoutputz --inoutput %srzOutput File Typez --xPrefExt %sFzPartial Volume Imagez--outPartial %s)rrrzExecution Timez --null %szSet default maximum heap sizez-xDefaultMem %drz(Set default maximum number of processes.z-xMaxProcess %d)rrrN)rrrrrRr r#r:rr%r&r' outPartialr+r,rr-r.r/r/r/r0rPs0 rc@seZdZedddZdS)&JistBrainPartialVolumeFilterOutputSpeczPartial Volume ImageT)rrN)rrrrrr/r/r/r0rpsrc@s(eZdZdZeZeZdZddiZ dZ dS)JistBrainPartialVolumeFilterz|Partial Volume Filter. Filters an image for regions of partial voluming assuming a ridge-like model of intensity. zVjava edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.brain.JistBrainPartialVolumeFilter rzoutPartial.niiTN) rrrr3rr4rr5r6r7r8r/r/r/r0rts rc@s eZdZeddddZeddddZeddddZejd d d d d Z ejddddd Z ejddddd Z ejdddd Z ej ejeddddZej ejeddddZej ejeddd dZej ejedd!d"dZejd#d$d Zejd%d&d Zejd'd(d)dd*Zd+S),$JistIntensityMp2rageMaskingInputSpeczSecond inversion (Inv2) ImageTz --inSecond %s)rrrz%Quantitative T1 Map (T1_Images) Imagez--inQuantitative %szT1-weighted (UNI) Imagez--inT1weighted %sZ exponentialz half-normalz`Model distribution for background noise (default is half-normal, exponential is more stringent).z--inBackground %s)rrrrzSkip zero valuesz --inSkip %sbinaryZprobazQWhether to use a binary threshold or a weighted average based on the probability.z--inMasking %srzOutput File Typez --xPrefExt %sFzSignal Proba Imagez--outSignal_Proba %s)rrrzSignal Mask Imagez--outSignal_Mask %szMasked T1 Map Imagez--outMasked_T1_Map %szMasked Iso Imagez--outMasked_T1weighted %szExecution Timez --null %szSet default maximum heap sizez-xDefaultMem %drz(Set default maximum number of processes.z-xMaxProcess %d)rrrN)rrrrrlZinQuantitativermr r#rrnZ inMaskingr%r&r' outSignal outSignal2rprqr+r,rr-r.r/r/r/r0rsh   rc@s<eZdZedddZedddZedddZedddZdS)%JistIntensityMp2rageMaskingOutputSpeczSignal Proba ImageT)rrzSignal Mask ImagezMasked T1 Map ImagezMasked Iso ImageN)rrrrrrrprqr/r/r/r0rs   rc@s.eZdZdZeZeZdZdddddZ dZ d S) JistIntensityMp2rageMaskingz8Estimate a background signal mask for a MP2RAGE dataset.zYjava edu.jhu.ece.iacl.jist.cli.run de.mpg.cbs.jist.intensity.JistIntensityMp2rageMasking zoutSignal2.niiz outSignal.niizoutMasked2.niiz outMasked.nii)rrrqrpTN) rrrr3rr4rr5r6r7r8r/r/r/r0rsrc@seZdZeeddddZejdddZejdd dZ ej d d d d dZ ej ddddZ eeddddZ ejdddZejdddZejdddddZdS),MedicAlgorithmThresholdToBinaryMaskInputSpecz Input volumesrz --inLabel %s)rrrzMinimum threshold value.z--inMinimum %f)rrzMaximum threshold value.z--inMaximum %frrz;Use the images max intensity as the max value of the range.z --inUse %srzOutput File Typez --xPrefExt %sz Binary Maskz--outBinary %szExecution Timez --null %szSet default maximum heap sizez-xDefaultMem %drz(Set default maximum number of processes.z-xMaxProcess %dT)rrrN)rrrr rZinLabelr r!r|rSr#rr%Z outBinaryr+r,rr-r.r/r/r/r0rs& rc@s eZdZdS)-MedicAlgorithmThresholdToBinaryMaskOutputSpecN)rrrr/r/r/r0rsrc@s$eZdZdZeZeZdZiZ dZ dS)#MedicAlgorithmThresholdToBinaryMaskz}Threshold to Binary Mask. Given a volume and an intensity range create a binary mask for values within that range. zqjava edu.jhu.ece.iacl.jist.cli.run edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThresholdToBinaryMask TN) rrrr3rr4rr5r6r7r8r/r/r/r0rs r)Cr3osbaserrrrrrr r r r r r1r2r9rBrCrDrJrKrLrOrPrQrXrYrZr\r]r^rirjrkrsrtrurxryrzr~rrrrrrrrrrrrrrrrrrrrrrrrrr/r/r/r0st0PO#  9   30  !!  X ^! B