/home/bennett/temp/temp10/out230002file:/home/bennett/temp/temp10/out2/falsexmlC:\catnapGC\aaaaOut.txttrue0File Collectionfalsetruetruebtxtlstbs0b0 Valuesfalsetruecombinebvals70.0150.016.0120.016.0120.0150.070.0UNKNOWN1.3 combinebvalsedu.jhu.ece.iacl.plugins.dti.DWICombineBvalTablestrueAlgorithm Informationfalsetrueb0FILETable of b-valuesfalsetrueb0Table of b-valuesfalsetrueCompute Mean B070.0150.0175.0291.0175.0291.0150.070.0Bennett Landmanlandman@jhu.eduJohn Bogovicbogovic@jhu.edu1.1.1.1 Converts a http://sites.google.com/site/jhupami/Johns Hopkins UniversityCompute Mean B0edu.jhu.ece.iacl.plugins.dti.ComputeMeanB0trueAlgorithm Informationfalsetruetruetiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp20Input Slab Collectionfalsetruetruetiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp20Volumes OutfalsetrueextractAllComponents70.0150.0400.0177.0400.0177.0150.070.0extractAllComponentsedu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractFileCollectionComponentstrueAlgorithm Informationfalsetruetruetiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp20Mult-Component Volume FileCollectionfalsetruetrue0File CollectionfalsetrueC:\catnapGC\aaaaOut.txtcsvtxt0/home/bennett/temp/01/recs.txtList Filefalsetrue001000000Offset Indexfalsetrue00100000Start Entryfalsetrue-1-1100000End Entryfalsetruefilecollectionlist70.0150.0363.06.0363.06.0150.070.0FileBasefilecollectionlistfalsetrueBasefilecollectionlistfalsetrue-13-10000000001000000000Dimension to ExtractfalsetrueExecution Timefalsetrueedu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractFileCollectionComponents1.16db97641-90aa-44a8-bffb-13fb92b63e05AlgorithmtruetrueIACL.Utilities.VolumeBaseextractAllComponentsfalsetrueedu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractFileCollectionComponents1.15a3b71d5-7c2d-4276-96f5-5b720f1ff2d3AlgorithmtruetrueBaseextractAllComponentsfalsetruetruetiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp20Source VolumesfalsetrueFileColReg70.0252.0137.0382.0137.0382.0252.070.0John Bogovicbogovic@jhu.edu1.1.1.1 Extract Components of each input volume. Organize the output as a FileCollectionhttp://sites.google.com/site/jhupami/Johns Hopkins UniversityFileColRegedu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistrationtrueAlgorithm Informationfalsetruetiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp20Target Volumefalsetrue-1-1-11tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16Mean B0 volumefalsetrue-1falsegrad0Gradient Tablefalsetruegrad0Table of Gradient Directionsfalsetruecombinegradvals70.0150.0194.0120.0194.0120.0150.070.01.1 combinegradvalsedu.jhu.ece.iacl.plugins.dti.DWICombineGradTablestrueAlgorithm Informationfalsetruetruetxtdpfgrad0Gradient Tablesfalsetruetrue0File CollectionfalsetrueC:\catnapGC\aaaaOut.txtcsvtxt0/home/bennett/temp/01/grads.txtList Filefalsetrue001000000Offset Indexfalsetrue00100000Start Entryfalsetrue-1-1100000End Entryfalsetruefilecollectionlist70.0150.0194.08.0194.08.0150.070.0FileBasefilecollectionlistfalsetrueBasefilecollectionlistfalsetrue-1Execution Timefalsetrueedu.jhu.ece.iacl.plugins.dti.DWICombineGradTables1.1146fe3e9-6db4-4de8-afb9-3612ef086373AlgorithmtruetrueIACL.DTIBasecombinegradvalsfalsetrueedu.jhu.ece.iacl.plugins.dti.DWICombineGradTables1.1e68af8fc-bcf5-4889-944b-36dbfa84efc9AlgorithmtruetrueBasecombinegradvalsfalsetruegraddpf0Table of diffusion weighting directionsfalsetrue-1-1Rigid - 6Global rescale - 7Specific rescale - 9Affine - 123Degrees of freedomfalsetrueCorrelation ratioLeast squaresNormalized cross correlationNormalized mutual information0Cost functionfalsetrueTrilinearBspline 3rd orderBspline 4th orderCubic LagrangianQuintic LagrangianHeptic LagrangianWindowed sinc0Registration interpolationfalsetrueTrilinearBspline 3rd orderBspline 4th orderCubic LagrangianQuintic LagrangianHeptic LagrangianWindowed sincNearest Neighbor0Output interpolationfalsetrueAllXYZ0Apply rotationfalsetrue-30.0-360.0360.0Minimum anglefalsetrue30.0-360.0360.0Maximum anglefalsetrue15.00.0360.0Coarse angle incrementfalsetrue6.00.0360.0Fine angle incrementfalsetrue10-10000000001000000000Multiple of tolerance to bracket the minimumfalsetrue2-10000000001000000000Number of iterationsfalsetrue3-10000000001000000000Number of minima from Level 8 to test at Level 4falsetruetrueUse the max of the min resolutions of the two datasets when resamplingfalsetruetrueSubsample image for speedfalsetruefalseSkip multilevel search (Assume images are close to alignment)falsetruetruemtx0Transformation Matricesfalsetruetruetiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp20Registered Volumesfalsetruetruetiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp20Input Volume FilesfalsetrueVolToCombined4DSlabs70.0150.0188.0469.0188.0469.0150.070.0Bennett Landmanlandman@jhu.eduJohn Bogovicbogovic@jhu.edu1.2 Converts a http://sites.google.com/site/jhupami/Johns Hopkins UniversityVolToCombined4DSlabsedu.jhu.ece.iacl.plugins.utilities.volume.VolumeCollectionToCombinedSlabCollectiontrueAlgorithm Informationfalsetrue41100Number of Slabsfalsetruetruetiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp20Output Combined Slabsfalsetruetruetiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp20DWI and Reference Image(s) Data (4D)falsetrueTensor Estimation: LLMSE70.0150.0165.0559.0165.0559.0150.070.0http://sites.google.com/site/bennettlandman/Bennett Landmanlandman@jhu.eduLandman BA, Farrell JA, Jones CK, Smith SA, Prince JL, Mori S. Effects of diffusion weighting schemes on the reproducibility of DTI-derived fractional anisotropy, mean diffusivity, and principal eigenvector measurements at 1.5T. Neuroimage 2007;36(4):1123-1138.Basser, PJ, Jones, DK. "Diffusion-tensor MRI: Theory, experimental design and data analysis - a technical review." NMR Biomed 2002; 15(7-8):456-671.1.1.1 Log-linear minium mean squared error tensor estimation.http://sites.google.com/site/jhupami/Johns Hopkins University, Department of Biomedical EngineeringTensor Estimation: LLMSEedu.jhu.ece.iacl.plugins.dti.DWITensorEstLLMSEtrueAlgorithm Informationfalsetruegraddpf0Table of diffusion weighting directionsfalsetruegrad0Corrected Gradient Tablefalsefalse-1b0Table of b-valuesfalsetrue-1falsetiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp20Mask Volume to Determine Region of Tensor Estimation (3D)falsetrueYesNo0Attempt to estimate tensors for voxels with missing data?falsetruetruetiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp20Tensor (xx,xy,xz,yy,yz,zz)falsetruetruetiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp20Input Slab CollectionfalsetrueCombined4DSlabsToVol70.0150.0155.0642.0155.0642.0150.070.0Bennett Landmanlandman@jhu.eduJohn Bogovicbogovic@jhu.edu1.1.1.1 Converts a http://sites.google.com/site/jhupami/Johns Hopkins UniversityCombined4DSlabsToVoledu.jhu.ece.iacl.plugins.utilities.volume.CombinedSlabCollectionToVolumeCollectiontrueAlgorithm InformationfalsetruetrueUse 4D Outputfalsetruetruetiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp20Output FileVolume Collectionfalsetrue-1-1-11tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk164D Output (optional)falsefalse-1-1-16tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16Tensor Volume (4D)falsetrueTensor : Compute DTI Contrasts70.0150.0203.0726.0203.0726.0150.070.0http://sites.google.com/site/bennettlandman/Bennett Landmanlandman@jhu.eduBasser, PJ, Jones, DK. "Diffusion-tensor MRI: Theory, experimental design and data analysis - a technical review." NMR Biomed 2002; 15(7-8):456-671.1.1.1 Estimates tensor contrasts.By default, estimates Mean Diffusion (MD), Fractional Anisotropy (FA), and the primary eigenvector (VEC1).Can optionally output all eigenvalues/vectors, as well as Relative Anisotropy (RA), and Volume Ratio (VR).http://sites.google.com/site/jhupami/Johns Hopkins University, Department of Biomedical EngineeringTensor : Compute DTI Contrastsedu.jhu.ece.iacl.plugins.dti.DWITensorContraststrueAlgorithm Informationfalsetrue<none>RA.VR0Additional Anisotropies:falsetrue<none>Eigen vectors/values0Additional Eigen-Contrasts:falsetrue-1-1-11FLOATtiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16FAfalsetrue-1-1-11tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16Scalar Weight Volume (3D)falsetrueTensor : Compute Color Encoded Map70.0150.0162.0811.0162.0811.0150.070.0http://sites.google.com/site/bennettlandman/Bennett Landmanlandman@jhu.eduBasser, PJ, Jones, DK. "Diffusion-tensor MRI: Theory, experimental design and data analysis - a technical review." NMR Biomed 2002; 15(7-8):456-671.1.1.1 Create an RGB colormap image from a scalar intensity weighted by a vectorUse a scalar volume (intensity in [0,1] to weight a vector volume (4-D, 4th dimension = x,y,z, in [-1 1]) to create a single RGB color volume. This is typically used with an FA weight an PEV vector.http://sites.google.com/site/jhupami/Johns Hopkins University, Department of Biomedical EngineeringTensor : Compute Color Encoded Mapedu.jhu.ece.iacl.plugins.dti.DWITensorColorEncodedMaptrueAlgorithm Informationfalsetrue-1-1-13tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16Vector direction to encoded color (4D)falsetrue-1-1-13tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16VEC1falsetrue-1-1-1-11COLORtiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16RGBfalsetrueExecution Timefalsetrueedu.jhu.ece.iacl.plugins.dti.DWITensorColorEncodedMap1.1693ccea4-738d-40a6-bbb0-d08998ee2c53AlgorithmtruetrueIACL.DTIBaseTensor : Compute Color Encoded Mapfalsetrueedu.jhu.ece.iacl.plugins.dti.DWITensorColorEncodedMap1.137fd4eaa-194e-4486-96b0-ca44b491861aAlgorithmtruetrueBaseTensor : Compute Color Encoded Mapfalsetrue-1-1-1-11tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16MDfalsetrue-1-1-11tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16RAfalsefalse-1-1-11tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16VRfalsefalse-1-1-13tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16Evalsfalsefalse-1-1-13tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16VEC2falsefalse-1-1-13tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16VEC3falsefalseExecution Timefalsetrueedu.jhu.ece.iacl.plugins.dti.DWITensorContrasts1.12d7f4074-a388-4ed9-87a3-806888d2f8f8AlgorithmtruetrueIACL.DTIBaseTensor : Compute DTI Contrastsfalsetrueedu.jhu.ece.iacl.plugins.dti.DWITensorContrasts1.10c9050f9-02d5-4100-8d15-9d287aa47e4aAlgorithmtruetrueBaseTensor : Compute DTI Contrastsfalsetrue-1Execution Timefalsetrueedu.jhu.ece.iacl.plugins.utilities.volume.CombinedSlabCollectionToVolumeCollection1.1658f500c-4646-4ce6-aa48-499f63b11374AlgorithmtruetrueIACL.Utilities.VolumeBaseCombined4DSlabsToVolfalsetrueedu.jhu.ece.iacl.plugins.utilities.volume.CombinedSlabCollectionToVolumeCollection1.1e3fc9149-d7dc-4ff5-a39c-5f4e2c781713AlgorithmtruetrueBaseCombined4DSlabsToVolfalsetrue-1Execution Timefalsetrueedu.jhu.ece.iacl.plugins.dti.DWITensorEstLLMSE1.1f9a712cd-c866-41dd-993c-27821b237fa7AlgorithmtruetrueModeling.DiffusionIACLTensor Estimation: LLMSEfalsetrueedu.jhu.ece.iacl.plugins.dti.DWITensorEstLLMSE1.139250d48-b156-4fb0-bbbf-db5df6321376AlgorithmtruetrueBaseTensor Estimation: LLMSEfalsetrue-1Execution Timefalsetrueedu.jhu.ece.iacl.plugins.utilities.volume.VolumeCollectionToCombinedSlabCollection1.168bb01d2-e146-4879-96f9-8f3e700f9ba8AlgorithmtruetrueIACL.Utilities.VolumeBaseVolToCombined4DSlabsfalsetrueedu.jhu.ece.iacl.plugins.utilities.volume.VolumeCollectionToCombinedSlabCollection1.1580c1bc1-7879-4b01-bcee-fdfcebcbe341AlgorithmtruetrueBaseVolToCombined4DSlabsfalsetrue-1Execution Timefalsetrueedu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration1.168dbadcc-b0d5-46af-972a-1fd47072d2acAlgorithmtruetrueBaseMainfalsetrueBaseAdvancedfalsetrueIACL.RegistrationBaseFileColRegfalsetrueedu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration1.17d1df9c8-3fc3-4d73-9b8f-15a4310c3981AlgorithmtruetrueBaseFileColRegfalsetrue-1-1trueRegister b0's ?falsetrueExecution Timefalsetrueedu.jhu.ece.iacl.plugins.dti.ComputeMeanB01.16dc403bd-1f8c-4c58-842d-b96d06947cc0AlgorithmtruetrueIACL.DTIBaseCompute Mean B0falsetrueedu.jhu.ece.iacl.plugins.dti.ComputeMeanB01.15e5e5aae-0a68-47b1-a582-47ab03df2217AlgorithmtruetrueBaseCompute Mean B0falsetrue-1Execution Timefalsetrueedu.jhu.ece.iacl.plugins.dti.DWICombineBvalTables1.1a6a8224f-abd7-4359-8a06-878dbb83354bAlgorithmtruetrueIACL.DTIBasecombinebvalsfalsetrueedu.jhu.ece.iacl.plugins.dti.DWICombineBvalTables1.1a235ff9b-7ee4-4483-be7b-dbd68facf88aAlgorithmtruetrueBasecombinebvalsfalsetrue-1/home/bennett/temp/01/bs.txtfile:/home/bennett/temp/01/bs.txtList Filefalsetrue001000000Offset Indexfalsetrue00100000Start Entryfalsetrue-1-1100000End Entryfalsetruefilecollectionlist70.0150.016.02.016.02.0150.070.0FileBasefilecollectionlistfalsetrueBasefilecollectionlistfalsetrue