/iacl/cruise08/bennett/kwyjibo/T1-proc 2024 4 file:/iacl/cruise08/bennett/kwyjibo/T1-proc/ false xml T1 : Double Angle 70.0 150.0 353.0 434.0 353.0 434.0 150.0 70.0 UNKNOWN Bennett Landman landman@jhu.edu 1.1 Estimate T1 from a double flip-angle experiment. Uses direct calculation. http://www.nitrc.org/projects/jist Johns Hopkins University, Department of Biomedical Engineering T1 : Double Angle edu.jhu.ece.iacl.plugins.quantitative.EstimateT1FromDoubleAngle true Algorithm Information 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 FILE Low Angle Volume (3D) 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 true Registered Volumes false true OARLinearRegistration1.2 70.0 266.0 131.0 293.0 131.0 293.0 266.0 70.0 Bjórn 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 1.2 Linear 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. OARLinearRegistration1.2 edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection true Algorithm Information 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 true Source Volumes 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 Volume false true csv txt 0 file:/iacl/cruise08/kwyjibo/raw/T1_15.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 vollist 70.0 150.0 64.0 96.0 64.0 96.0 150.0 70.0 Volume Base vollist false true Base vollist 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 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 Volume false true file:/iacl/cruise08/kwyjibo/raw/T1_60.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 vollist 70.0 150.0 361.0 26.0 361.0 26.0 150.0 70.0 Volume Base vollist false true Base vollist 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 Target volume false true OARLinearRegistration1.2 70.0 266.0 553.0 292.0 553.0 292.0 266.0 70.0 Algorithm Information 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 true Source Volumes 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 Volume false true file:/iacl/cruise08/kwyjibo/raw/T1_60.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 vollist 70.0 150.0 380.0 204.0 380.0 204.0 150.0 70.0 Volume Base vollist false true Base vollist 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 Reference Weighted volume 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 Input Weighted volume false false Rigid - 6 Global rescale - 7 Specific rescale - 9 Affine - 12 0 Degrees of freedom false true Correlation ratio Least squares Normalized cross correlation Normalized mutual information 2 Cost function false true Trilinear Bspline 3rd order Bspline 4th order Cubic Lagrangian Quintic Lagrangian Heptic Lagrangian Windowed sinc 1 Registration interpolation false true Trilinear Bspline 3rd order Bspline 4th order Cubic Lagrangian Quintic Lagrangian Heptic Lagrangian Windowed sinc Nearest Neighbor 1 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 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 4 4 4 4 Transformation Matrix false false txt csv xfm 0 Transformation Matrices false false true mtx xfm 0 Transformations 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 true Registered Volumes 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 High Angle Volume (3D) false true 0 Execution Time false true edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection 1.1 4d373aa1-3650-4862-ae4b-450e6be9ec82 Algorithm true true Base Main false true Base Advanced false true Registration IACL OARLinearRegistration1.2 false true edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection 1.1 9c3a5edd-c7eb-4396-9b9c-f21349b0dc04 Algorithm true true Base OARLinearRegistration1.2 false true -1 -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 Reference Weighted volume 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 Input Weighted volume false false Rigid - 6 Global rescale - 7 Specific rescale - 9 Affine - 12 0 Degrees of freedom false true Correlation ratio Least squares Normalized cross correlation Normalized mutual information 2 Cost function false true Trilinear Bspline 3rd order Bspline 4th order Cubic Lagrangian Quintic Lagrangian Heptic Lagrangian Windowed sinc 1 Registration interpolation false true Trilinear Bspline 3rd order Bspline 4th order Cubic Lagrangian Quintic Lagrangian Heptic Lagrangian Windowed sinc Nearest Neighbor 1 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 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 4 4 4 4 Transformation Matrix false false txt csv xfm 0 Transformation Matrices false false true mtx xfm 0 Transformations false true Execution Time false true edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection 1.1 091e56d4-e549-4224-a946-dd04a46603c9 Algorithm true true Base Main false true Base Advanced false true Registration IACL OARLinearRegistration1.2 false true edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection 1.1 d28e14e2-5f66-415f-81f4-d4298cec0b90 Algorithm true true Base OARLinearRegistration1.2 false true 0 15.0 -1.0E20 1.0E20 Low Flip Angle (deg) false true 60.0 -1.0E20 1.0E20 High Flip Angle (deg) false true 100.0 -1.0E20 1.0E20 Repetition Time (TR, ms) 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 T1Est false true Base Parameters false true csv txt 0 Summary File false true copy_summary File Name false true 0 DIRECTORY file:/iacl/cruise08/bennett/kwyjibo/quantitative/ Destination Directory false false true Append Experiment Name false true copy 70.0 150.0 338.0 560.0 338.0 560.0 150.0 70.0 Output Base copy false true Base copy false true -1 Execution Time false true edu.jhu.ece.iacl.plugins.quantitative.EstimateT1FromDoubleAngle 1.1 b93de4de-127f-472d-add1-f05354154f85 Algorithm true true Quantitative IACL T1 : Double Angle false true edu.jhu.ece.iacl.plugins.quantitative.EstimateT1FromDoubleAngle 1.1 32c4379d-eb06-4a6b-95f9-a9b848ca88c3 Algorithm true true Base T1 : Double Angle false true