/iacl/cruise08/bennett/kwyjibo/T2-proc20244file:/iacl/cruise08/bennett/kwyjibo/T2-proc/falsexml-1-1-11tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16FILEVolumefalsetrue-1-1-1-1tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16Mult-Component Volumefalsetrueextract_vol_comp70.0150.047.0199.047.0199.0150.070.0UNKNOWNextract_vol_compedu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractVolumeComponenttrueAlgorithm Informationfalsetrue001000000Start Indexfalsetrue101000000End IndexfalsetruetrueSplit output volumes?falsetrue-1-1-1-1tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16Extracted Volumefalsefalse-1-1-1-1tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16falseExtracted and Split Volumesfalsetrue-1-1-1-1tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16trueSource VolumesfalsetrueOARLinearRegistration1.270.0266.0121.0311.0121.0311.0266.070.0Bjórn Hamre "Three-dimensional image registration of magnetic resonance (MRI) head volumes" Section for Medical Image Analysis and Informatics Department of Physiology & Department of Informatics University of Bergen, Norway. FLIRT, at http://www.fmrib.ox.ac.uk/fsl/flirt/ Powell method to find the global minimum: http://math.fullerton.edu/ mathews/n2003/PowellMethodMod.html 1.2Linear Registration algorithm based on FLIRT. Finds a linear transformation bringing the source volume into the space of the target volume. Degrees of freedom can be specified.OARLinearRegistration1.2edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollectiontrueAlgorithm Informationfalsetrue-1-1-11tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16Target volumefalsetrue-1-1-11tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16Volumefalsetruecsvtxt0file:/iacl/cruise08/kwyjibo/raw/matchedT2-MPR.txtList Filefalsetrue001000000Offset Indexfalsetrue00100000Start Entryfalsetrue-1-1100000End Entryfalsetruevollist70.0150.0361.026.0361.026.0150.070.0VolumeBasevollistfalsetrueBasevollistfalsetrue-1-1-1-1tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16Volume to Match - Dimensions & Resolutionfalsefalsetrans_vol70.0210.0460.0448.0460.0448.0210.070.01.3 Applies a given transformation matrix to a volumetric image using the specified interpolation methodtrans_voledu.jhu.ece.iacl.plugins.registration.MedicAlgorithmTransformVolumetrueAlgorithm Informationfalsetrue-1-1-1-1tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16trueVolumesfalsetrue-1TrilinearBspline 3rd orderBspline 4th orderCubic LagrangianQuintic LagrangianHeptic LagrangianWindowed sincNearest Neighbor1Registration interpolationfalsetrue1.0-1.0E201.0E20xfalsetrue1.0-1.0E201.0E20yfalsetrue1.0-1.0E201.0E20zfalsetrueResolutionsfalsetrue256-10000000001000000000xfalsetrue256-10000000001000000000yfalsetrue198-10000000001000000000zfalsetrueDimensionsfalsetrue1.00.00.00.00.01.00.00.00.00.01.00.00.00.00.01.04444Transformation Matrixfalsefalse0.00.00.00.00.00.00.00.00.00.00.00.00.00.00.00.04444Transformation Matrixfalsefalse-1falsemtx0Transformation MatricesfalsetruefalseInvert MatrixfalsetruetrueRotate Around CenterfalsetruefalseUse Anatomical CenterfalsetruetrueUpdate OriginfalsetruefalseUse Scanner Anatomical TransformfalsetruefalseCropfalsetruefalsePadfalsetrue0-10000000001000000000Pad Valuefalsetrue-1-1-1-1tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16trueTransformed Volumesfalsetrue-1-1-12tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16Dual Echo Volume (4D)falsetrueT2 : Dual Echo70.0150.0238.0545.0238.0545.0150.070.0Bennett Landmanlandman@jhu.edu1.1 Estimate T2 from a two-point fit using dual echo imaging. Uses direct calculation from the log of the ratio of the observed signals.http://www.nitrc.org/projects/jistJohns Hopkins University, Department of Biomedical EngineeringT2 : Dual Echoedu.jhu.ece.iacl.plugins.quantitative.EstimateT2FromDualEchotrueAlgorithm Informationfalsetrue28.2-1.0E201.0E20First Echo TE (ms)falsetrue80.0-1.0E201.0E20Second Echo TE (ms)falsetrue-1-1-11FLOATtiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16T2EstfalsetrueExecution Timefalsetrueedu.jhu.ece.iacl.plugins.quantitative.EstimateT2FromDualEcho1.15c7a92c3-cb28-4d69-912f-89e3c4696da9AlgorithmtruetrueQuantitativeIACLT2 : Dual Echofalsetrueedu.jhu.ece.iacl.plugins.quantitative.EstimateT2FromDualEcho1.1b2be0c36-54ca-4119-aa99-1128063b85baAlgorithmtruetrueBaseT2 : Dual Echofalsetrue0Execution Timefalsetrueedu.jhu.ece.iacl.plugins.registration.MedicAlgorithmTransformVolume1.1eae43f43-c206-429c-9aa2-bda94fcab96aAlgorithmtruetrueRegistrationIACLtrans_volfalsetrueedu.jhu.ece.iacl.plugins.registration.MedicAlgorithmTransformVolume1.1e0501634-ec36-41df-aef6-0f814b0939d6AlgorithmtruetrueBasetrans_volfalsetrue-1-1-1-1-11tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16Reference Weighted volumefalsefalse-1-1-11tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16Input Weighted volumefalsefalseRigid - 6Global rescale - 7Specific rescale - 9Affine - 120Degrees of freedomfalsetrueCorrelation ratioLeast squaresNormalized cross correlationNormalized mutual information2Cost functionfalsetrueTrilinearBspline 3rd orderBspline 4th orderCubic LagrangianQuintic LagrangianHeptic LagrangianWindowed sinc1Registration interpolationfalsetrueTrilinearBspline 3rd orderBspline 4th orderCubic LagrangianQuintic LagrangianHeptic LagrangianWindowed sincNearest Neighbor1Output 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)falsetruetxtcsvxfm0Transformation Matricesfalsefalsetruemtxxfm0Transformationsfalsetrue-1-1-1-1tiftifflsmstkjpegjpgbmpgifpictpicpngpsddibtgaxbmxpmxmlpcxicocurmghmgzrawimgniinhdrnrrdimadcmbinmapmncaviimcolyqtmovheadbrikicsidshdrspmfitsdm3tmgmrcwusiggednologctinfoinfo~voiafniparparv2recfrecjp2vtk16trueRegistered VolumesfalsetrueExecution Timefalsetrueedu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection1.191128250-15e1-4e63-a829-a8a67b0359c8AlgorithmtruetrueBaseMainfalsetrueBaseAdvancedfalsetrueRegistrationIACLOARLinearRegistration1.2falsetrueedu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection1.1a2222676-c419-47b2-8cb7-ba939d7ef250AlgorithmtruetrueBaseOARLinearRegistration1.2falsetrue-1Execution Timefalsetrueedu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractVolumeComponent1.148840e43-05c8-45c0-b7c3-77279de2619bAlgorithmtruetrueIACL.Utilities.VolumeBaseextract_vol_compfalsetrueedu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractVolumeComponent1.105ac4083-f039-41f8-9ed2-9862598e0a6aAlgorithmtruetrueBaseextract_vol_compfalsetrue-1file:/iacl/cruise08/kwyjibo/raw/matchedT2-DE.txtList Filefalsetrue001000000Offset Indexfalsetrue00100000Start Entryfalsetrue-1-1100000End Entryfalsetruevollist70.0150.033.040.033.040.0150.070.0VolumeBasevollistfalsetrueBasevollistfalsetrue