/home/bennett/temp/temp10/out2 3000 2 file:/home/bennett/temp/temp10/out2/ false xml C:\catnapGC\aaaaOut.txt true 0 File Collection false true true b txt lst bs 0 b0 Values false true combinebvals 70.0 150.0 16.0 120.0 16.0 120.0 150.0 70.0 UNKNOWN 1.3 combinebvals edu.jhu.ece.iacl.plugins.dti.DWICombineBvalTables true Algorithm Information false true b 0 FILE Table of b-values false true b 0 Table of b-values false true Compute Mean B0 70.0 150.0 175.0 291.0 175.0 291.0 150.0 70.0 Bennett Landman landman@jhu.edu John Bogovic bogovic@jhu.edu 1.1.1.1 Converts a http://sites.google.com/site/jhupami/ Johns Hopkins University Compute Mean B0 edu.jhu.ece.iacl.plugins.dti.ComputeMeanB0 true Algorithm Information false true true tif 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 0 Input Slab Collection false true true tif 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 0 Volumes Out false true extractAllComponents 70.0 150.0 400.0 177.0 400.0 177.0 150.0 70.0 extractAllComponents edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractFileCollectionComponents true Algorithm Information false true true tif 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 0 Mult-Component Volume FileCollection false true true 0 File Collection false true C:\catnapGC\aaaaOut.txt csv txt 0 /home/bennett/temp/01/recs.txt List File false true 0 0 1000000 Offset Index false true 0 0 100000 Start Entry false true -1 -1 100000 End Entry false true filecollectionlist 70.0 150.0 363.0 6.0 363.0 6.0 150.0 70.0 File Base filecollectionlist false true Base filecollectionlist false true -1 3 -1000000000 1000000000 Dimension to Extract false true Execution Time false true edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractFileCollectionComponents 1.1 6db97641-90aa-44a8-bffb-13fb92b63e05 Algorithm true true IACL.Utilities.Volume Base extractAllComponents false true edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractFileCollectionComponents 1.1 5a3b71d5-7c2d-4276-96f5-5b720f1ff2d3 Algorithm true true Base extractAllComponents false true true tif 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 0 Source Volumes false true FileColReg 70.0 252.0 137.0 382.0 137.0 382.0 252.0 70.0 John Bogovic bogovic@jhu.edu 1.1.1.1 Extract Components of each input volume. Organize the output as a FileCollection http://sites.google.com/site/jhupami/ Johns Hopkins University FileColReg edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration true Algorithm Information false true tif 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 0 Target Volume false true -1 -1 -1 1 tif 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 vtk 16 Mean B0 volume false true -1 false grad 0 Gradient Table false true grad 0 Table of Gradient Directions false true combinegradvals 70.0 150.0 194.0 120.0 194.0 120.0 150.0 70.0 1.1 combinegradvals edu.jhu.ece.iacl.plugins.dti.DWICombineGradTables true Algorithm Information false true true txt dpf grad 0 Gradient Tables false true true 0 File Collection false true C:\catnapGC\aaaaOut.txt csv txt 0 /home/bennett/temp/01/grads.txt List File false true 0 0 1000000 Offset Index false true 0 0 100000 Start Entry false true -1 -1 100000 End Entry false true filecollectionlist 70.0 150.0 194.0 8.0 194.0 8.0 150.0 70.0 File Base filecollectionlist false true Base filecollectionlist false true -1 Execution Time false true edu.jhu.ece.iacl.plugins.dti.DWICombineGradTables 1.1 146fe3e9-6db4-4de8-afb9-3612ef086373 Algorithm true true IACL.DTI Base combinegradvals false true edu.jhu.ece.iacl.plugins.dti.DWICombineGradTables 1.1 e68af8fc-bcf5-4889-944b-36dbfa84efc9 Algorithm true true Base combinegradvals false true grad dpf 0 Table of diffusion weighting directions false true -1 -1 Rigid - 6 Global rescale - 7 Specific rescale - 9 Affine - 12 3 Degrees of freedom false true Correlation ratio Least squares Normalized cross correlation Normalized mutual information 0 Cost function false true Trilinear Bspline 3rd order Bspline 4th order Cubic Lagrangian Quintic Lagrangian Heptic Lagrangian Windowed sinc 0 Registration interpolation false true Trilinear Bspline 3rd order Bspline 4th order Cubic Lagrangian Quintic Lagrangian Heptic Lagrangian Windowed sinc Nearest Neighbor 0 Output interpolation false true All X Y Z 0 Apply rotation false true -30.0 -360.0 360.0 Minimum angle false true 30.0 -360.0 360.0 Maximum angle false true 15.0 0.0 360.0 Coarse angle increment false true 6.0 0.0 360.0 Fine angle increment false true 10 -1000000000 1000000000 Multiple of tolerance to bracket the minimum false true 2 -1000000000 1000000000 Number of iterations false true 3 -1000000000 1000000000 Number of minima from Level 8 to test at Level 4 false true true Use the max of the min resolutions of the two datasets when resampling false true true Subsample image for speed false true false Skip multilevel search (Assume images are close to alignment) false true true mtx 0 Transformation Matrices false true true tif 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 0 Registered Volumes false true true tif 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 0 Input Volume Files false true VolToCombined4DSlabs 70.0 150.0 188.0 469.0 188.0 469.0 150.0 70.0 Bennett Landman landman@jhu.edu John Bogovic bogovic@jhu.edu 1.2 Converts a http://sites.google.com/site/jhupami/ Johns Hopkins University VolToCombined4DSlabs edu.jhu.ece.iacl.plugins.utilities.volume.VolumeCollectionToCombinedSlabCollection true Algorithm Information false true 4 1 100 Number of Slabs false true true tif 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 0 Output Combined Slabs false true true tif 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 0 DWI and Reference Image(s) Data (4D) false true Tensor Estimation: LLMSE 70.0 150.0 165.0 559.0 165.0 559.0 150.0 70.0 http://sites.google.com/site/bennettlandman/ Bennett Landman landman@jhu.edu Landman 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):456-67 1.1.1.1 Log-linear minium mean squared error tensor estimation. http://sites.google.com/site/jhupami/ Johns Hopkins University, Department of Biomedical Engineering Tensor Estimation: LLMSE edu.jhu.ece.iacl.plugins.dti.DWITensorEstLLMSE true Algorithm Information false true grad dpf 0 Table of diffusion weighting directions false true grad 0 Corrected Gradient Table false false -1 b 0 Table of b-values false true -1 false tif 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 0 Mask Volume to Determine Region of Tensor Estimation (3D) false true Yes No 0 Attempt to estimate tensors for voxels with missing data? false true true tif 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 0 Tensor (xx,xy,xz,yy,yz,zz) false true true tif 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 0 Input Slab Collection false true Combined4DSlabsToVol 70.0 150.0 155.0 642.0 155.0 642.0 150.0 70.0 Bennett Landman landman@jhu.edu John Bogovic bogovic@jhu.edu 1.1.1.1 Converts a http://sites.google.com/site/jhupami/ Johns Hopkins University Combined4DSlabsToVol edu.jhu.ece.iacl.plugins.utilities.volume.CombinedSlabCollectionToVolumeCollection true Algorithm Information false true true Use 4D Output false true true tif 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 0 Output FileVolume Collection false true -1 -1 -1 1 tif 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 vtk 16 4D Output (optional) false false -1 -1 -1 6 tif 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 vtk 16 Tensor Volume (4D) false true Tensor : Compute DTI Contrasts 70.0 150.0 203.0 726.0 203.0 726.0 150.0 70.0 http://sites.google.com/site/bennettlandman/ Bennett Landman landman@jhu.edu Basser, PJ, Jones, DK. "Diffusion-tensor MRI: Theory, experimental design and data analysis - a technical review." NMR Biomed 2002; 15(7-8):456-67 1.1.1.1 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 Engineering Tensor : Compute DTI Contrasts edu.jhu.ece.iacl.plugins.dti.DWITensorContrasts true Algorithm Information false true <none> RA.VR 0 Additional Anisotropies: false true <none> Eigen vectors/values 0 Additional Eigen-Contrasts: false true -1 -1 -1 1 FLOAT tif 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 vtk 16 FA false true -1 -1 -1 1 tif 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 vtk 16 Scalar Weight Volume (3D) false true Tensor : Compute Color Encoded Map 70.0 150.0 162.0 811.0 162.0 811.0 150.0 70.0 http://sites.google.com/site/bennettlandman/ Bennett Landman landman@jhu.edu Basser, PJ, Jones, DK. "Diffusion-tensor MRI: Theory, experimental design and data analysis - a technical review." NMR Biomed 2002; 15(7-8):456-67 1.1.1.1 Create an RGB colormap image from a scalar intensity weighted by a vector Use 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 Engineering Tensor : Compute Color Encoded Map edu.jhu.ece.iacl.plugins.dti.DWITensorColorEncodedMap true Algorithm Information false true -1 -1 -1 3 tif 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 vtk 16 Vector direction to encoded color (4D) false true -1 -1 -1 3 tif 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 vtk 16 VEC1 false true -1 -1 -1 -1 1 COLOR tif 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 vtk 16 RGB false true Execution Time false true edu.jhu.ece.iacl.plugins.dti.DWITensorColorEncodedMap 1.1 693ccea4-738d-40a6-bbb0-d08998ee2c53 Algorithm true true IACL.DTI Base Tensor : Compute Color Encoded Map false true edu.jhu.ece.iacl.plugins.dti.DWITensorColorEncodedMap 1.1 37fd4eaa-194e-4486-96b0-ca44b491861a Algorithm true true Base Tensor : Compute Color Encoded Map false true -1 -1 -1 -1 1 tif 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 vtk 16 MD false true -1 -1 -1 1 tif 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 vtk 16 RA false false -1 -1 -1 1 tif 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 vtk 16 VR false false -1 -1 -1 3 tif 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 vtk 16 Evals false false -1 -1 -1 3 tif 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 vtk 16 VEC2 false false -1 -1 -1 3 tif 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 vtk 16 VEC3 false false Execution Time false true edu.jhu.ece.iacl.plugins.dti.DWITensorContrasts 1.1 2d7f4074-a388-4ed9-87a3-806888d2f8f8 Algorithm true true IACL.DTI Base Tensor : Compute DTI Contrasts false true edu.jhu.ece.iacl.plugins.dti.DWITensorContrasts 1.1 0c9050f9-02d5-4100-8d15-9d287aa47e4a Algorithm true true Base Tensor : Compute DTI Contrasts false true -1 Execution Time false true edu.jhu.ece.iacl.plugins.utilities.volume.CombinedSlabCollectionToVolumeCollection 1.1 658f500c-4646-4ce6-aa48-499f63b11374 Algorithm true true IACL.Utilities.Volume Base Combined4DSlabsToVol false true edu.jhu.ece.iacl.plugins.utilities.volume.CombinedSlabCollectionToVolumeCollection 1.1 e3fc9149-d7dc-4ff5-a39c-5f4e2c781713 Algorithm true true Base Combined4DSlabsToVol false true -1 Execution Time false true edu.jhu.ece.iacl.plugins.dti.DWITensorEstLLMSE 1.1 f9a712cd-c866-41dd-993c-27821b237fa7 Algorithm true true Modeling.Diffusion IACL Tensor Estimation: LLMSE false true edu.jhu.ece.iacl.plugins.dti.DWITensorEstLLMSE 1.1 39250d48-b156-4fb0-bbbf-db5df6321376 Algorithm true true Base Tensor Estimation: LLMSE false true -1 Execution Time false true edu.jhu.ece.iacl.plugins.utilities.volume.VolumeCollectionToCombinedSlabCollection 1.1 68bb01d2-e146-4879-96f9-8f3e700f9ba8 Algorithm true true IACL.Utilities.Volume Base VolToCombined4DSlabs false true edu.jhu.ece.iacl.plugins.utilities.volume.VolumeCollectionToCombinedSlabCollection 1.1 580c1bc1-7879-4b01-bcee-fdfcebcbe341 Algorithm true true Base VolToCombined4DSlabs false true -1 Execution Time false true edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration 1.1 68dbadcc-b0d5-46af-972a-1fd47072d2ac Algorithm true true Base Main false true Base Advanced false true IACL.Registration Base FileColReg false true edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration 1.1 7d1df9c8-3fc3-4d73-9b8f-15a4310c3981 Algorithm true true Base FileColReg false true -1 -1 true Register b0's ? false true Execution Time false true edu.jhu.ece.iacl.plugins.dti.ComputeMeanB0 1.1 6dc403bd-1f8c-4c58-842d-b96d06947cc0 Algorithm true true IACL.DTI Base Compute Mean B0 false true edu.jhu.ece.iacl.plugins.dti.ComputeMeanB0 1.1 5e5e5aae-0a68-47b1-a582-47ab03df2217 Algorithm true true Base Compute Mean B0 false true -1 Execution Time false true edu.jhu.ece.iacl.plugins.dti.DWICombineBvalTables 1.1 a6a8224f-abd7-4359-8a06-878dbb83354b Algorithm true true IACL.DTI Base combinebvals false true edu.jhu.ece.iacl.plugins.dti.DWICombineBvalTables 1.1 a235ff9b-7ee4-4483-be7b-dbd68facf88a Algorithm true true Base combinebvals false true -1 /home/bennett/temp/01/bs.txt file:/home/bennett/temp/01/bs.txt List File false true 0 0 1000000 Offset Index false true 0 0 100000 Start Entry false true -1 -1 100000 End Entry false true filecollectionlist 70.0 150.0 16.0 2.0 16.0 2.0 150.0 70.0 File Base filecollectionlist false true Base filecollectionlist false true