40952file:/fs1/masi/data/3T/ParRec_27Jul101202/proc/dti/falsexmlMod-1-Extract_b_and_grad_from_PAR_filesedu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmExtract b and grad from PAR filesExtract_b_and_grad_from_PAR_files110.0123.0150.070.0edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollectionExtract b and grad from PAR filesExtract_b_and_grad_from_PAR_filesExtract b and grad from PAR filesfalsetruenull3Modeling.DiffusionIACLedu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeaderAlgorithmAlgorithmAlgorithmtruetruenulledu.jhu.ece.iacl.plugins.hardi.ExtractBvalGradFromPAR1.116b650d3-6b1c-4286-bfc8-f799adebac6cedu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformationAlgorithm InformationAlgorithm InformationAlgorithm InformationfalsetruenullBennett Landmanlandman@jhu.eduhttp://sites.google.com/site/bennettlandman/null1.4Extract b/grad tables from new (modern 4.2+ PAR files).Extract b/grad tables from new (modern 4.2+ PAR files).http://www.nitrc.org/projects/jist/Johns Hopkins UniversityExtract_b_and_grad_from_PAR_filesExtract b and grad from PAR filesedu.jhu.ece.iacl.plugins.hardi.ExtractBvalGradFromPARRCfalseedu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollectionPar filesPar filesPar filesfalsetruenullpar PAR parv2 PARv2 0nulledu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollectionExtract b and grad from PAR filesExtract_b_and_grad_from_PAR_filesExtract b and grad from PAR filesfalsetruenull4nullBaseedu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeaderAlgorithmAlgorithmAlgorithmtruetruenulledu.jhu.ece.iacl.plugins.hardi.ExtractBvalGradFromPAR1.16ecfa054-9223-4b2f-b722-1c0ad83fb6afedu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileb-Valuesb-Valuesb-ValuesfalsetruenullFILEnullnullb 0edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileGradient TablesGradient TablesGradient TablesfalsetruenullFILEnullnullgrad 0edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPerformanceExecution TimeExecution TimeExecution 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Listvollist365.053.0150.070.0edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollectionREC Volulme ListvollistVolulme File Listfalsetruenull4VolumeBaseedu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileList FileList FileList FilefalsetruenullFILEnullfile:/fs1/masi/data/3T/ParRec_27Jul101202/dti.txtcsv txt 0edu.jhu.ece.iacl.jist.pipeline.parameter.ParamIntegerOffset IndexOffset IndexOffset Indexfalsetruenull001000000edu.jhu.ece.iacl.jist.pipeline.parameter.ParamIntegerStart EntryStart EntryStart Entryfalsetruenull00100000edu.jhu.ece.iacl.jist.pipeline.parameter.ParamIntegerEnd EntryEnd EntryEnd Entryfalsetruenull-1-1100000edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollectionVolulme File ListvollistVolulme File Listfalsetruenull1nullBaseedu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeVolumeVolumeVolumefalsetruenullFILEnullnulltif tiff lsm stk jpeg jpg bmp gif pict pic png psd dib tga xbm xpm xml pcx ico cur mgh mgz raw img nii nhdr nrrd ima dcm bin map mnc avi imc oly qt mov head brik ics ids hdr spm fits dm3 tmg mrc wu sig gedno log ct info info~ voi afni par parv2 rec frec jp2 gz bz2 vtk 16edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter-1-1-11null0Mod-4-CATNAPedu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmCATNAPCATNAP174.0343.0378.070.0edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollectionCATNAPCATNAPCATNAPfalsetruenull6DTIMASIedu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeaderAlgorithmAlgorithmAlgorithmtruetruenulledu.vanderbilt.masi.plugins.dti.CATNAP1.19b26ed8d-0687-4152-ae32-63e28cb08995edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformationAlgorithm InformationAlgorithm InformationAlgorithm InformationfalsetruenullBennett 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Registrationfalsetruenull4RegistrationIACLedu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeaderAlgorithmAlgorithmAlgorithmtruetruenulledu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration1.18a9de523-cf94-4211-baf0-89fc30e7cf4fedu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformationAlgorithm InformationAlgorithm InformationAlgorithm InformationfalsetruenullJohn Bogovicbogovic@jhu.edunullnull1.11 Extract Components of each input volume. Organize the output as a FileCollectionnullhttp://www.nitrc.org/projects/jist/Johns Hopkins UniversityFileColRegFile Collection Efficient Registrationedu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistrationUNKNOWNtrueedu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollectionMainMainMainfalsetruenull12nullBaseedu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollectionSource VolumesSource VolumesSource Volumestruetruenulltif tiff lsm stk jpeg jpg bmp gif pict pic png psd dib tga xbm xpm xml pcx ico cur mgh mgz raw img nii nhdr nrrd ima dcm bin map mnc avi imc oly qt mov head brik ics ids hdr spm fits dm3 tmg mrc wu sig gedno log ct info info~ voi afni par parv2 rec frec jp2 gz bz2 vtk 16edu.jhu.ece.iacl.jist.io.ImageDataReaderWriternull-1-1-1-1edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeTarget VolumeTarget VolumeTarget VolumetruetruenullFILEnullnulltif tiff lsm stk jpeg jpg bmp gif pict pic png psd dib tga xbm xpm xml pcx ico cur mgh mgz raw img nii nhdr nrrd ima dcm bin map mnc avi imc oly qt mov head brik ics ids hdr spm fits dm3 tmg mrc wu sig gedno log ct info info~ voi afni par parv2 rec frec jp2 gz bz2 vtk 16edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter-1-1-11null0edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollectionGradient TableGradient TableGradient Tabletruefalsenullgrad 0nulledu.jhu.ece.iacl.jist.pipeline.parameter.ParamOptionDegrees of freedomDegrees of freedomDegrees of freedomfalsetruenullRigid - 6Global rescale - 7Specific rescale - 9Affine - 123edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOptionCost functionCost functionCost functionfalsetruenullCorrelation ratioLeast squaresNormalized cross correlationNormalized mutual information3edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOptionRegistration interpolationRegistration interpolationRegistration interpolationfalsetruenullTrilinearBspline 3rd orderBspline 4th orderCubic LagrangianQuintic LagrangianHeptic LagrangianWindowed sinc1edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOptionOutput interpolationOutput interpolationOutput interpolationfalsetruenullTrilinearBspline 3rd orderBspline 4th orderCubic LagrangianQuintic LagrangianHeptic LagrangianWindowed sincNearest Neighbor1edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOptionApply rotationApply rotationApply rotationfalsetruenullAllXYZ0edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDoubleMinimum angleMinimum angleMinimum anglefalsetruenull-30.0-360.0360.0edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDoubleMaximum angleMaximum angleMaximum anglefalsetruenull30.0-360.0360.0edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDoubleCoarse angle incrementCoarse angle incrementCoarse angle incrementfalsetruenull15.00.0360.0edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDoubleFine angle incrementFine angle incrementFine angle incrementfalsetruenull6.00.0360.0edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollectionAdvancedAdvancedAdvancedfalsetruenull7nullBaseedu.jhu.ece.iacl.jist.pipeline.parameter.ParamIntegerMultiple of tolerance to bracket the minimumMultiple of tolerance to bracket the minimumMultiple of tolerance to bracket the minimumfalsetruenull10-10000000001000000000edu.jhu.ece.iacl.jist.pipeline.parameter.ParamIntegerNumber of iterationsNumber of iterationsNumber of iterationsfalsetruenull2-10000000001000000000edu.jhu.ece.iacl.jist.pipeline.parameter.ParamIntegerNumber of minima from Level 8 to test at Level 4Number of minima from Level 8 to test at Level 4Number of minima from Level 8 to test at Level 4falsetruenull3-10000000001000000000edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBooleanUse the max of the min resolutions of the two datasets when resamplingUse the max of the min resolutions of the two datasets when resamplingUse the max of the min resolutions of the two datasets when resamplingfalsetruenulltrueedu.jhu.ece.iacl.jist.pipeline.parameter.ParamBooleanSubsample image for speedSubsample image for speedSubsample image for speedfalsetruenulltrueedu.jhu.ece.iacl.jist.pipeline.parameter.ParamBooleanSkip multilevel search (Assume images are close to alignment)Skip multilevel search (Assume images are close to alignment)Skip multilevel search (Assume images are close to alignment)falsetruenulltrueedu.jhu.ece.iacl.jist.pipeline.parameter.ParamBooleanMultithreading for RegistrationMultithreading for RegistrationMultithreading for RegistrationfalsetrueSet to false by default, this parameter controls the multithreaded behavior of the linear registration.falseedu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollectionVolCollect to Combined4DSlabCollectSlabVolCollect to Combined4DSlabCollectfalsetruenull4Utilities.VolumeIACLedu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeaderAlgorithmAlgorithmAlgorithmtruetruenulledu.jhu.ece.iacl.plugins.utilities.volume.VolumeCollectionToCombinedSlabCollection1.18a42d162-fef5-4f6c-b713-98017a3b6c1eedu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformationAlgorithm InformationAlgorithm InformationAlgorithm InformationfalsetruenullBennett Landmanlandman@jhu.edunullJohn Bogovicbogovic@jhu.edunullnull1.11Converts VolumeCollection to CombinedSlabCollection. Splits each volume in the input collection into a number of smaller volumes "slabs". The user can specify the number of slabswith the "Number of Slabs" input. The output collection will have numSlabs volumes, each of which will have N components in the fourth image dimension (where N is the number of input volumes).Converts VolumeCollection to CombinedSlabCollection. Splits each volume in the input collection into a number of smaller volumes "slabs". The user can specify the number of slabswith the "Number of Slabs" input. The output collection will have numSlabs volumes, each of which will have N components in the fourth image dimension (where N is the number of input volumes).http://www.nitrc.org/projects/jist/Johns Hopkins UniversityVolCollect_to_Combined4DSlabCollectVolCollect to Combined4DSlabCollectedu.jhu.ece.iacl.plugins.utilities.volume.VolumeCollectionToCombinedSlabCollectionRCfalseedu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollectionInput Volume FilesInput Volume FilesInput Volume Filestruetruenulltif tiff lsm stk jpeg jpg bmp gif pict pic png psd dib tga xbm xpm xml pcx ico cur mgh mgz raw img nii nhdr nrrd ima dcm bin map mnc avi imc oly qt mov head brik ics ids hdr spm fits dm3 tmg mrc wu sig gedno log ct info info~ voi afni par parv2 rec frec jp2 gz bz2 vtk 16edu.jhu.ece.iacl.jist.io.ImageDataReaderWriternull-1-1-1-1edu.jhu.ece.iacl.jist.pipeline.parameter.ParamIntegerNumber of SlabsNumber of SlabsNumber of Slabsfalsetruenull41100edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollectionFiber Tracker (FACT)FACTFiber Tracker (FACT)falsetruenull10Modeling.TractographyIACLedu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeaderAlgorithmAlgorithmAlgorithmtruetruenulledu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberTracker1.11113c3f5-56d2-4755-afd1-4767e87451e2edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformationAlgorithm InformationAlgorithm InformationAlgorithm InformationfalsetruenullBennett Landmanlandman@jhu.eduhttp://sites.google.com/site/bennettlandman/John Bogovicbogovic@jhu.edunullMori S, Crain BJ, Chacko VP, van Zijl PCM, "Three dimensional tracking of axonal projections in the brain by magnetic resonance imaging" Ann Neurol. 1999. 45:(265-9)null1.4FACT - Deteriministic, Streamline Tractography Algorithm.FACT - Deteriministic, Streamline Tractography Algorithm.An implementation of the FACT algorithm. By default, begins tracking at all voxels, but can optionally track from a single seed point. Returns a fiber collection in DTIStudio and in VTK format.nullJohns Hopkins University, Departments of Electrical and Biomedical EngineeringFiber_Tracker_FACTFiber Tracker (FACT)edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberTrackerRCfalseedu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeFractional AnisotropyFractional AnisotropyFractional AnisotropytruetruenullFILEnullnulltif tiff lsm stk jpeg jpg bmp gif pict pic png psd dib tga xbm xpm xml pcx ico cur mgh mgz raw img nii nhdr nrrd ima dcm bin map mnc avi imc oly qt mov head brik ics ids hdr spm fits dm3 tmg mrc wu sig gedno log ct info info~ voi afni par parv2 rec frec jp2 gz bz2 vtk 16edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter-1-1-11FLOAT0edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeVector FieldVector FieldVector FieldtruetruenullFILEnullnulltif tiff lsm stk jpeg jpg bmp gif pict pic png psd dib tga xbm xpm xml pcx ico cur mgh mgz raw img nii nhdr nrrd ima dcm bin map mnc avi imc oly qt mov head brik ics 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