Bayesian Data-Analysis Toolbox

Release 4.23, Manual Version 3

G. Larry Bretthorst
Biomedical MR Laboratory
Washington University School Of Medicine,
Campus Box 8227
Room 2313, East Bldg.,
4525 Scott Ave.
St. Louis MO 63110
http://bayes.wustl.edu
Email: [email protected]

September 18, 2018

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[15] G. Larry Bretthorst, William C. Hutton, Joel R. Garbow, and Joseph J.H. Ackerman (2005),
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“How accurately can parameters from exponential models be estimated? A Bayesian view,”
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[22] André d’Avignon, G. Larry Bretthorst, Marilyn Emerson Holtzer, and Alfred Holtzer (1999),
“Thermodynamics and Kinetics of a Folded-Folded Transition at Valine-9 of a GCN4-Like
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Lisa Mints, and Alfred Holtzer (2001), “Temperature Dependence of the Folding and Unfolding
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Analysis of Exponential Decay Data: An Example Taken from Intravoxel Incoherent Motion
Experiments,” Magn. Reson. in Med., 29, pp. 642–647.
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Index

Ak definition, 349 Data, 423

Hj` (ti ) definition, 349 Reports
λ` definition, 349 Bayes Accepted, 425
gjk eigenvalue, 349 Console Log, 425
McMC Values, 425
Abscissa, 437 Using, 425
Computational, 436 Viewers
Generating, 427 Fortran/C Models, 423
Loading, 39 Image, 423
Multicolumn, 437 Prior Probabilities, 425
Number Of Columns, 458 Widgets
Total Data Values, 456 Build, 423
Aliases, 113, 126 Find Outliers, 423
Amplitudes orthonormal definition, 349 Get Statistics, 425
Analyze Image Pixel Package, 411 System, 423
Modification History, 413 User, 423
Phased Images, 397 Ascii Data Viewer, 53
Reports Assigning Probabilities, 118
Bayes Accepted, 413
Using, 413 Bandwidth, 111, 127
Viewers Bayes Analyze Package, 155
Fortran/C Models, 411 Levenberg-Marquardt , 171
Image, 411 Step, 194
Prior Probabilities, 413 Algorithm, 175
Widgets Amplitudes, 197, 198
Abscissa File, 411 Bayes Model, 159, 161
Build, 411 Bayesian Calculations, 167
Find Outliers, 411 Bruker, 162
Get Statistics, 413 Build BA Model, 159
System, 411 Covariance, 174
User, 411 Default Parameters Settings, 155
Analyze Image Pixel Unique Package, 423 Error Messages, 200
Highlight Fid Model Viewer, 160
Abscissa, 425 Interface, 156
Data, 425 Likelihood
Input Image Gaussian, 158
Abscissa, 423 Student’s t-distribution, 158

484
INDEX 485

Log File, 193, 195 bayes.probabilities.nnnn File, 177, 190, 190

Lorentzian lineshape, 161 bayes.status.nnnn File, 177, 196, 200
Marking Resonances, 157 bayes.summary1.nnnn File, 177, 198, 198
Model bayes.summary2.nnnn File, 177, 199, 199
Jo , 165 bayes.summary3.nnnn File, 177, 200, 200
Jp , 165 Global Parameters, 182, 183
Js , 165 Model File, 184
Amplitude, 163, 164 Probabilities file, 191
Bessel Function, 163 Zero Order Phase, 182
Constants Models, 157 Parameter File
Correlated, 157, 162, 164 Activate Shims, 180
Equation, 161, 164, 164 Analysis Directory, 178
First Order Phase, 157, 162, 164 By Fid, 181
First Point, 162, 164 Data Type, 180
Gaussian, 163 Default Model, 181
Imaginary Constant, 164 Directory Organization, 180
Multi-Exponential, 163 Fid Model Name, 178
Multiple Data Sets, 165 File Version, 178
Multiplet Order, 164 First Fid, 181
Multiplet Orders, 164 First Order Phase, 180, 183
Multiplets, 162 Imaginary Constant, 184
Multiplets of Multiplets, 164 Last Fid, 181
Non-Lorentzian, 163 lb, 182
Offsets, 162 Maximum Candidates, 182
Real Constant, 164 Maximum New Resonances, 182
Relative Amplitude, 164–166 Model Fid Number, 181
Resonance Frequency, 165 Model Name, 184
Shim Order, 163 Model Names, 181
Shimming, 166 Model Number, 184
Shimming Order, 164 Model Points, 181
Uncorrelated, 157, 162, 164 Multiplets of Multiplets, 185
Zero Order Phase, 157, 162, 164 Noise Start, 181
Model Interface, 160 Numerical Parameters, 178
Multiplets, 158 Output Format, 180
Newton-Raphson, 171 Prior Odds, 182
Noise File, 158 Procpar, 178
Noise Standard Deviation, 158 Real Constant, 184
Outputs Relative Amplitude, 183
Bayes.accepted File, 177 Resonance Model, 185
bayes.log.nnnn File, 177, 193, 193 Shim Order, 182
bayes.model.nnnn File, 177, 185, 197, 197 Spectrometer Frequency, 182
bayes.noise File, 180 Text Parameters, 178
bayes.noise.nnnn File, 158, 180 Total Complex Data Values, 181
bayes.output.nnnn File, 176, 186, 186 Total Data Values, 181
bayes.params File, 176, 177 Total Sampling Time, 182
bayes.params.nnnn File, 176, 177, 177 True Reference, 182
486 INDEX

Units, 180 To, 158, 176

Use Noise StdDev, 180 Bayes Find Resonances Package, 239
User Reference, 182 Bayesian Calculations, 241
Prior Probabilities, 167 Current Fid, 239
Probabilities File, 191 Model Equation, 241
Product Rule, 168 Number of data sets, 239
Relative Amplitude, 167 Phase Model
Remove Resonances, 159 Automatic, 239, 242
Reports Common, 239, 242
Bayes Status, 155 Independent, 239, 242
Save/Reset, 159 Prior Probabilities, 243–245
Search, 166 Reports
Levenberg-Marquardt , 166 Bayes Accepted, 241, 246
Short Parameter Description, 195 Condensed, 246
Siemens, 162 Console log, 246
Status File, 196 McMC Values, 246
Steepest Descents, 173 Prob Model, 246
Sum Rule, 168 Using, 239, 241
Summary File, 198 Viewers
Summary Reports, 176 Fid Data, 240
Summary2, 199 Fid Model, 240, 246
Summary3, 201 File, 246
Units, 161 Plot Results, 246
Using, 157 Text, 246
Varian/Agilent, 162 Widgets
Widgets, 155 Build FID Model, 240, 241, 246
By, 158, 176 Constant, 239, 242
First Point, 157, 163 First Trace, 239
From, 158, 176 Last Trace, 239
Imag Offset, 163 Model Fid Number, 241
Imaginary Offset, 157 Phase Model, 239, 242
Mark, 159 Bayes Home Directory, 45, 49
Max New Res, 157 Bayes Manual pdf, 469
New, 159 Bayes Metabolite Package
Noise, 158 Widgets
Phase, 157 Shift Left, 222
Primary, 158 Shift Right, 222
Real Offset, 157, 163 Bayes Metabolite Package, 219
Remove, 159 Aligning Resonances, 221
Remove All, 159 Bayesian Calculation, 225
Reset, 159, 193 Metabolite Locations, 221
Restore, 159 Model Equation, 223
Save, 159 Reports
Secondary, 159 Bayes Accepted, 221, 238
Shim Order, 157, 163 Condensed, 238
Signal, 158 Console log, 238
INDEX 487

McMC Values, 238 Bayes’ Theorem, 100, 139, 145, 153, 167, 211,
Prob Model, 238 226, 243, 252, 261, 269, 278, 288, 295,
Viewers 306, 314, 315, 317, 318, 331, 333, 343,
Fid Data, 219 370, 399, 407, 439
Fid Model, 221, 236 Bayes.accepted
File, 222, 238 Body, 77
Metabolite, 221 Header, 76
Plot Results, 238 Behrens-Fisher Package, 311
Text, 238 Bayesian Calculations
Widgets Derived Probabilities, 320
Fid Model, 221 Different Mean And Same Variance, 318
Fid Model Viewer, 221 Different Mean And Variance, 319
Load System Metabolite File, 219 Parameter Estimation, 321
Load System Resonance File, 221 Same Mean And Different Variance, 317
Load User Metabolite File, 219 Same Mean And Variance, 315
Load User Resonance File, 221 Model Equation
Shift Left, 221 Different Mean And Same Variance, 318
Shift Right, 221 Different Mean And Variance, 319
Bayes Model, 159, 159 Same Mean And Different Variance, 317
Bayes Test Data Package, 427 Same Mean And Variance, 315
Parameters, 431 Number of data sets, 311
Reports Parameter Listing, 323
Bayes Accepted, 428 Prior Probabilities
Condensed, 429 Different Mean And Same Variance, 318
McMC Values, 429, 431–433 Different Mean And Variance, 319
Viewers Same Mean And Different Variance, 317
Fortran/C Models, 427 Same Means And Same Variance, 315
Image, 428 Reports
Prior Probabilities, 427 Bayes Accepted, 311, 322
Text Data, 430 Condensed, 322
Text Results, 429 Console Log, 322, 323
Widgets McMC Values, 322, 323
# Images, 427 Prob Model, 322
# Slices, 427 Using, 311
Abscissa, 427 Viewers
ArrayDim, 427 File, 322
Build, 427 Plot Results, 322, 324
Get Job, 428 Prior Probabilities, 311
Max Value, 427 Text, 322
Noise SD, 427 Widgets
Parameter Ranges, 428 None, 311
Pe, 427 Big Endian, 471, 473
Ro, 427 Big Magnetization Transfer Package, 259
Run, 428 Bayesian Calculations, 259
Set (server), 428 Files
Status, 428 Bayes Analyze, 264
488 INDEX

Fid, 263 Binned Density Function Estimation, 355

Peak Pick, 262 Binned Histogram Package
Model Equation, 261 Reports
Number of data sets, 259 Bayes Accepted, 357
Prior Probabilities, 261 Viewers
Reports Ascii, 355
Bayes Accepted, 259, 262 Binned Histograms Package
Condensed, 262 Using, 357
Console log, 262 Viewers
McMC Values, 262 Prior Probabilities, 355
Prob Model, 262 Bloch-McConnell Equations, 267, 277
Using, 259
Viewers Changing the Bayes Home Directory, 469
Ascii Data, 259 Compilers, 29
File, 262 CC, 29, 455
Prior Probabilities, 259 Fortran, 29, 455
Text, 262 Correlations, 91
Widgets
Find Outliers, 259 Diffusion Tensor Package, 247
Big Peak/Little Peak Package, 207 Ascii File Formats, 247, 254, 255
Bayesian Calculations, 209 Bayesian Calculations, 249
Fid Analyzed, 207 Prior Probabilities
Model Equation, 210 ∆, 254
Metabolites, 209 Γ, 254
Solvent, 210 δ, 254
Number of data sets, 207 σ, 253
Prior Probabilities Amplitudes, 253
Metabolite, 207 Eigenvalues, 253
Solvent, 207 Euler Angles, 253
Removing Resonances, 207 Likelihood, 253
Reports Parameter, 254
Bayes Accepted, 209, 216 Reports
Condensed, 216 Bayes Accepted, 247, 255
Console log, 216 Condensed, 255
McMC Values, 216 Console log, 255
Prob Model, 216 McMC Values, 255
Using, 207 Prob Model, 255
Viewers Symmetries, 253
File, 216 Using, 247
Model, 209 Viewers
Plot Results, 216 File, 247, 255
Prior Probabilities, 207 Plot Results, 255
Text, 216 Prior Probabilities, 247, 253
Widgets Text, 255
Metabolite, 207 Widgets
Solvent, 207 Abscissa Options, 248
INDEX 489

Find Outliers, 247 With Marginalization, 347

Include Constant, 247, 248, 255 Output Names
Tensor Number, 247, 248, 255 Derived, 354
Use b Matrix, 255 Parameters, 353
Use b Vectors, 255 Reports
Use g Vectors, 254 Bayes Accepted, 343, 353
Discrete Fourier Transform, 110, 113, 123 Condensed, 353
Console log, 353
Enter Ascii Model Package, 329 McMC Values, 353
Bayesian Calculations, 332 Params File, 353
Marginalization, 332 Prob Model, 353
No Marginalization, 331 Using, 343
Fortran/C Models, 330, 335 Viewers
Model Equation Ascii Data, 341
Marginalization, 331 File, 353
No Marginalization, 331 Fortran/C Models, 341
Output Names Plot Results, 353
Derived, 335 Prior Probabilities Not Used, 341
Parameters, 335 Text, 353
Reports Widgets
Bayes Accepted, 331, 335 Build Not Used, 341
Bayes Params, 335 Find Outliers, 341
Condensed, 335 System, 341
Console log, 335 User, 341
McMC Values, 335 Errors In Variables Package, 303
Prob Model, 335 Ascii File Formats
Using, 331 Errors In X and Y Known, 303, 309
Viewers Errors In X Known, 303, 309
Ascii Data, 329 Errors In Y Known, 303, 309
File, 335 Errors Unknown, 303, 309
Fortran/C Models, 329 Bayesian Calculations, 305
Plot Results, 335 Data Error Bars, 303
Prior Probabilities, 329 Files
Text, 335 Ascii, 303
Widgets Bayes Analyze, 303
Build, 329 Peak Pick, 303
Find Outliers, 329 Model Equation, 305
System, 329 Number of data sets, 303
User, 329 Reports
Enter Ascii Model Selection Package, 341 Bayes Accepted, 305, 309
Bayesian Calculations Condensed, 309
Marginalization, 346 Console log, 309
No Marginalization, 344 McMC Values, 309
Fortran/C Models, 341, 343, 353 Prob Model, 309
Model Equation, 343 Using, 305
No Marginalization, 343 Viewers
490 INDEX

Ascii Data, 303 Varian fid, 36

File, 309 Fortran/C Models, 42, 455, 457, 458, 465–
Plot Results, 309 467
Text, 309 Images
Widgets 4dfp, 38
Given Errors In, 303 Binary, 38
Order, 303 Bruker 2dseq, 38
Exponentials Bruker stack, 38
Given Package, 137 DICOM, 38
Inversion Recovery Package, 151 FDF, 38
Magnetization Transfer Package, 267 Multi-Column Text, 38
Unknown Number of Package, 143 Siemens IMA, 38
k-space
Fid Data Viewer, 53 Text, 36
Fid Model Viewer, 68 Varian fid, 36
File Format mcmc.values, 76, 449
Ascii, 436 Model Listing, 77
File Viewer, 80 prob.model, 76
Files procpar, 470
4dfp, 59, 428, 430, 470, 471 Raw, 36
Header, 473 RDA, 36
Reading, 471 Statistics, 65
Abscissa, 39, 77, 470 System.err.txt, 469
afh, 53 System.out.txt, 469
ASCII, 35, 36 Varian fid, 36
Ascii, 53, 54, 435 WaterViscosityTable, 469
k-space, 437 Fortran/C Model Viewer, 93
Abscissa, 435, 436, 437 Popup Editor, 93
Data, 435 Fortran/C Models, 42, 330, 335, 353, 455
Image, 436 Abscissa, 463
Bayes Analyze, 36 Body, 463
Bayes.accepted, 51, 76 Abscissa, 457
Bayes.params, 76, 79 Declarations, 462
Bayes.prob.model, 447 Derived Parameters, 457, 459, 463
BayesManual.pdf, 469 Edit/Create New Model, 42, 455
Condensed, 77, 78 I/O, 464
Console.log, 76, 79, 465 Marginalization, 464
dir.info, 470 Gj (Ω, ti ), 464
fid, 470, 470 Amplitude Range, 465
ASCII, 36 Example, 465, 466
ffh, 56 Model Vectors, 465
Model, 68, 70 Ordering Amplitudes, 465
procpar, 470 Parameter File, 465, 467
Siemens Raw, 36 Parameter Order, 465
Siemens Rda, 36 Parameters, 465
Spectroscopic, 53 Model Files, 455
INDEX 491

Model Selection, 464 Constant, 137, 139

No Marginalization, 457 Find Outliers, 137
S(ti ), 455 Given Order, 27
Example, 456 Include Constant, 27
Parameter File, 458, 459, 465 Order, 137, 139
Parameters, 463 Given Polynomial Order Package, 285
Signal, 463 Bayesian Calculations, 288
Subroutine Interface, 460 Files
Abscissa, 462 Ascii, 285
Current Set, 460 Bayes Analyze, 285
Derived Parameters, 461 Peak Pick, 285
Maximum No Of Data Values, 461 Gram-Schmidt, 287
Number Of Abscissa Columns, 461 Model Equation, 287
Number Of Data Columns, 461 Number of data sets, 285
Number Of Derived Parameters, 461 Prior Probabilities, 289
Number Of Model Vectors, 461 Reports
Number Of Parameters, 460 Bayes Accepted, 285, 291
Parameters, 461 Condensed, 291
Signal, 462 Console log, 291
Total Complex Data Values, 461 McMC Values, 291
Subroutines and Functions, 464 Prob Model, 291
Frequency Estimation, 114, 132 Scatter Plots, 292
Using, 285
Given Exponential Package, 137 Viewers
Bayesian Calculations, 140 File, 290
Files Plot Results, 291
Ascii, 137 Text, 290
Bayes Analyze, 137 Widgets
Peak Pick, 137 Set Order, 285
Model Equation, 139
Number of data sets, 139 Histograms
Prior Probabilities, 139–141 Binned, 381
Reports Kernel Density, 381
Bayes Accepted, 137, 141
Condensed, 141 Image Model Selection Package, 415
Console log, 141 Abscissa, 415
McMC Values, 141 Fortran/C Models, 415, 417
Prob Model, 141 Reports
Symmetries, 141, 148 Bayes Accepted, 417
Using, 137 Using, 417
Viewers Viewers
File, 141 Fortran/C Models, 415
Plot Results, 141 Image, 415
Prior Probabilities, 137, 139 Widgets
Text, 141 Noise SD, 415
Widgets System, 415
492 INDEX

Use Gaussian, 415 Number of data sets, 364

User, 415 Plots
Image Viewer, 59 Expected Density Function, 367, 368
Images Mean Density Function, 367, 368
Flip Posterior Probability for the Kernel Type,
Horizontal, 63 365
Vertical, 63 Posterior Probability for the Number Of
Grayscale, 63 Kernels, 366
ImageJ, 63 Scatter Plots of Model Averaged Density
Original, 63 Function, 368
Inversion Recovery Package, 151 Standard Deviation of the Mean Density
Bayesian Calculations, 153 Function, 367, 368
Model Equation, 153 Prior Probabilities
Number of data sets, 153 Kernel Center, 371
Prior Probabilities, 153 Kernel Smoothing Parameter, 371
Reports Kernel Type, 370
Bayes Accepted, 151, 154 Number Of Kernels, 370
Condensed, 154 Reports
Console Log, 154 Bayes Accepted, 364
McMC Values, 154 Condensed, 372
Prob Model, 154 McMC Values, 372
Using, 151 Prob Model, 372
Viewers Using, 364
Plot Results, 154 Viewers
Prior Probability, 151 Ascii, 361
Widgets Widgets
Find Outliers, 151 Kernel Type, 364
Output Size, 364
Kernel Density Function Package, 361
Ascii File Format, 361 Levenberg-Marquardt, 171
Bayesian Calculations, 369 Linear Phasing Package, 395, 409
Data Requirements, 361 Interface, 397
Data, Model And Residuals, 369 Model Equation, 398
Kernels, 369 Widgets
Biweight, 362 cf, 403
Cosine, 362 Display, 403
Epanechnikov, 362 Display Array Element, 403
Exponential, 362 fn, 403
Gaussian, 362, 370 fn1, 403
nonnegative, 361 Image Type, 402
Real Valued, 361 Load An Image, 402
Triangular, 362 np, 403
Tricube, 362 nv, 403
Triweight, 362 Process, 403
Uniform, 362 Load Working Directory, 33
Likelihood, 371 Logical Independence, 117
INDEX 493

Magnetization Transfer Kinetics Package, 275 Viewers

Arrhenius Plot, 281 Ascii Data, 265
Bayesian Calculation, 278 Fid Data, 272
Boltzmann’s Constant, 277 File, 271
Eyring Equation, 275, 276, 277, 280 Plot Results, 262, 272, 281
Model Equation, 277 Prior Probabilities, 265
Plank’s Constant, 277 Text, 271
Prior Probabilities, 279 Widgets
Reports Find Outliers, 265
Bayes Accepted, 277, 281 Marginalization, 100
Condensed, 281 Bayes Analyze Package, 174
Console log, 281 Behrens-Fisher, 315
McMC Values, 281 Big Magnetization Transfer, 261
Prob Model, 281 Big Peak/Little Peak, 211
Sum and Difference Variables, 280 Diffusion Tensors, 252
Transmission coefficient, 277 Enter Ascii Model Package, 331
Universal Gas Constant, 277 Errors In Variables, 306
Using, 277 Fortran/C Models, 464
van’t Hoff Plot, 281 Given Exponential, 139
Viewers Inversion Recovery, 153
Ascii File, 275 Linear Phasing, 399
File, 281 Magnetization Transfer, 269
Prior Probabilities, 275 Magnetization Transfer Kinetics, 278
Text, 281 Metabolic Analysis, 225
Widgets Nonexhaustive Hypotheses, 101
Load, 275, 281 Nuisance Hypotheses, 100
Set, 275 Nuisance Parameter, 100
Uncertainty, 275 Unknown Number of Exponentials, 146
Magnetization Transfer Package, 265 Markov chain Monte Carlo, 132, 439
Bayesian Calculations, 267 Acceptance Rate, 444
Files Annealing Schedule, 91, 442
Ascii, 265 Dynamic, 443
Bayes Analyze, 265 Linear, 442
Inversion Recovery, 272 Killing Simulations, 443
Peak Pick, 265 Maximum Posterior Probability, 91
Model Equation, 267 Metropolis-Hastings, 439
Number of data sets, 265 Mixing, 91
Prior Probabilities, 265, 270 Monte Carlo Integration, 440
Reports Multiple Simulations, 441
Bayes Accepted, 267, 272 Posterior Probability, 440
Condensed, 272 Random Number Generators, 440
Console log, 272 Repeats, 91
McMC Values, 272 Sampling, 91
Prob Model, 272 Simulated Annealing, 442
Three Column Data, 265 the Proposal, 444
Using, 267
494 INDEX

MaxEnt Density Function Estimation Package, Siemens IMA, 37, 38

373 Single-Column Text, 38
Data Requirements, 381 Spectroscopic Fid, 35
Plots Test Data, 35, 39
Contour/Scatter, 375, 379 Text k-space, 36
Number Of Multipliers, 375, 378 Text k-space fid, 37
Reports User Manual, 35, 39
Bayes Accepted, 375 Help, 24
Console Log, 375 Packages, 22, 24, 33, 40
Using, 375 Settings, 46
Viewers Add Server, 48
Ascii, 373 Auto Configure Server, 48
Plot, 375, 378 McMC Parameters, 24, 46, 48
Prior Probabilities, 373 Min Annealing Steps, 48, 48
Widgets Port number, 48
Histogram Size, 373 Preferences, 49, 63
Order, 373 Remove Server, 48, 49
Maximum Entropy Method Of Moments, 102, Repetitions, 46, 48
377, 381 Server Name, 48
Advantages, 386 Server Setup, 24, 26, 48
Problems, 386 Set Window Size, 49
Review, 381 Simulations, 46, 48
Maximum Entropy Method Of Moments Package View Server Installation Info, 48, 49
Bayesian Calculations, 387 Spectroscopy fid, 36
Plots Utilities, 24, 50
Data, Model and Residuals, 380 Memory Monitor, 50
Menus Software Updates, 50
Files, 24, 35 System Information, 50
4dfp, 37, 38 WorkDir
Abscissa, 35, 39 Creating, 22, 33, 46
ASCII, 35, 36 Deleting, 22, 33, 46
Binary, 38 List, 24, 46
Bruker, 37 Loading, 46
Bruker 2dseq, 38 Name, 46
Bruker Stack, 38 Popup, 47
DICOM, 37, 38 Model Comparison
FDF, 37, 38 Big Peak/Little Peak Package, 211
fid, 36, 37 model orthonormal definition, 349
General Binary, 37 Mouse
Images, 35 Control-left, 59
Import Working Directories in Batch, 40 Fid Data Viewer
Import Working Directory, 40 Left, 56
Load Images, 36, 37, 59 Right, 56
Load Working Directory, 35 Shift-left, 59
Multi-Column Text, 37, 38 Multiplets
Save Working Directory, 35, 39 J-Coupling
INDEX 495

Center, 159 Image Pixel Model Selection, 22, 45

Primary, 159 Inversion Recovery, 20, 40, 151
Secondary, 159 Kernel Density Function, 361
Linear Phasing, 21, 44, 395
Newton-Raphson, 171 Magnetization Transfer, 20, 42, 265
Noise Standard Deviation, 64 Magnetization Transfer Kinetics, 20, 43, 275
Non-Linear Phasing Package, 405 Maximum Entropy Method Of Moments, 21,
Calculations, 407 44, 373
Model Equation, 405, 407 Metabolic Analysis, 21, 43, 219
Widgets Non-Linear Image Phasing, 21, 45, 405
Process, 409 Polynomials
Write Ascii images, 409 of Given Order, 21, 44
Write imaginary images, 409 of Unknown Order, 21, 44
Nuisance Parameter, 100, 115, 135 Test ASCII Model, 42
Nyquist Critical Frequency, 111, 127 Test Ascii Model, 20, 337
Unknown Number of Exponentials, 20, 40,
orthonormal, 349 143
Outliers, 475 Unknown Polynomial Order, 293
Mean Parameter, 477 Parameter File, 42
Model, 475 Number Of
Prob Number of, 476 Abscissa, 458
Proposal, 475 Data Columns, 458
Red dot, 477 Model Vectors, 458
Weighted Average, 477 Priors, 458
Prior Probability, 459
Packages
Amplitude, 460
Analyze Image Pixel Unique, 423
High, 459
Bayes Analyze, 20, 43, 57, 155, 200
Low, 459
Bayes Find Resonances, 21, 239
Mean, 459
Bayes Test Data, 427
NonLinear, 460
Behrens-Fisher, 21, 44, 311
Ordered, 460
Big Magnetization Transfer, 20, 43, 259
Parameter File, 459
Big Peak/Little Peak, 20, 43, 207
Peak, 459
Binned Density Function Estimation, 355
Prior Type, 460
Binned Histograms, 21, 44
Standard Deviation, 459
Diffusion Tensors, 20, 40, 247
Phase Cycling, 162
Enter ASCII Model, 42
Plot Results Viewer, 71
Enter Ascii Model, 20, 329
Plots
Enter ASCII Model Selection, 42
Data and Model, 81
Enter Ascii Model Selection, 20, 341
Data, Model and Residuals, 81
Errors In Variables, 21, 44, 303
Expected Log Likelihood, 88
Find Resonances, 43
Logarithm of the Posterior Probability, 91
Given Exponential, 20, 40, 137
Maximum Entropy Histogram, 84
Given Polynomial Order, 285
Maximum Entropy Histograms, 83
Image Model Selection, 415
McMC Samples, 83, 85
Image Pixel, 21, 45, 411
Parameter Vs Posterior Probability, 86, 87
496 INDEX

Posterior Probability, 82 Standard Deviations, 453

Posterior Probability Vs Parameter Value, Restoring An Analysis, 22, 35, 40
86 ROI
Residuals, 81 Expanding, 63
Scatter, 88, 91 Pixels, 63
png graphics, 59 Point, 62
Posterior Probability Vs Parameter Value, 86 Polygon, 62
Power Spectrum, 112, 123, 124 Square, 62
Prior Probabilities
Bayes Phase, 399 Saving An Analysis, 35, 39
Big Magnetization Transfer, 261 Schuster Periodogram, 112, 123
Big Peak/Little Peak, 212 Screen Captures, 49
Diffusion Tensor, 253 Settings
Enter Ascii Model, 331, 333 httpd server, 19
Errors In Variables, 306 Software
Magnetization Transfer, 269 Bayes Account, 29
Magnetization Transfer Kinetics, 279 CC, 29
Non-Linear Phasing Package Fortran, 29
A, 408 Installation, 29
θ, 408 javaws, 29
Prior Probability, 42, 65, 65 OS requirements, 29
Exponential, 67, 459 root requirements, 30
Gaussian, 67, 104, 106, 459 Start Up Window, 22, 33
Jeffreys’, 118 Steepest Descents, 173
Normalization Constant, 67 Subdirectories, 469
Parameter, 68, 459 Bayes, 39
Positive, 68, 460 Bayes.model.fid, 470
Uniform, 67, 103, 118, 459 Bayes.Predefined.Spec, 469
Prior Viewer, 65, 93 Bayes.test.data, 39
Probabilities BayesAnalyzeFiles, 470
Expected Log Likelihood, 453 BayesAsciiModels, 93, 469
Likelihood, 453 BayesOtherAnalysis, 35, 73, 470
Posterior, 453 fid, 36, 53
Prior, 453 images, 36, 38, 39, 59, 470
Product Rule, 99, 119, 344, 439 model.compile, 470
plugins, 470
Referencing Properties, 470
Setting, 59 Resources, 470
Reports Spectroscopic
Accepted File, 76 fid, 470
McMC Values File Working Directories, 470
General Description, 449 Subroutine Names, 464
Maximum Posterior Probability Simula- Sufficient Statistics, 122
tions, 451 Definition, 105
Mean Values, 452 Location Parameter, 108
Prior, 450 Sum Rule, 100, 119, 344, 440
INDEX 497

Test Ascii Model Package, 337 Condensed, 299

Reports Console Log, 298, 299
Bayes Accepted, 339 McMC Values, 299
Mcmc Values, 339 Polynomial Order Plot , 301
Using, 339, 428 Prob Model, 299
Viewers Using, 293
Ascii Data, 337 Viewers
Fortran/C Models, 337 File, 299
Prior Probabilities, 337 Text, 299
Widgets Widgets
Build, 337 Set Order, 293, 294
Find Outliers, 339 Unknown Order, 293, 294
System, 337
User, 337 Viewers, 27, 52
Thermodynamic Integration, 445, 449 ASCII Data, 36
Ascii Data, 27, 53, 56, 63, 137, 265, 275,
Uninstall, 49 285, 293, 311, 329, 337, 341
Unknown Number of Exponentials Package, 143 Expanding Plot, 53
Bayesian Calculations, 145 Printing, 53
Model Equation, 145 Right click, 53
Reports Bayes Model, 160
Bayes Accepted, 143, 148 Fid Data, 27, 265
Condensed, 148 fid Data, 53, 53, 285, 293
Console Log, 148, 149 Auto Range, 59
McMC Values, 148 Autoscale, 56
Prob Model, 148 Clear Cursors, 56
Using, 143 Clear Data, 57
Viewers Copy, 59
File, 148 Cursor, 56
Plot Results, 149, 150 Data Info, 57
Prior, 143 Expand, 56
Text, 148 fn, 57
Widgets Full, 56
Constant, 143 Get Peak, 56
Find Outliers, 143 Phase Popup, 57
Order, 143 Print, 59
Unknown Polynomial Order Package, 293 Properties, 59
Bayesian Calculations, 295 Referencing, 59
Files Save As, 57, 59
Ascii, 293 Set Preference, 57
Bayes Analyze, 293 Units, 59
Peak Pick, 293 Zoom, 59
Model Equation, 295 Fid Model, 27
Number of data sets, 293 fid Model, 68, 186
Reports Build BA Model, 70, 159
Bayes Accepted, 293, 299 Data, 71
498 INDEX

Horizontal, 71 Prior Probabilities, 138, 312

Model, 71 Text, 141, 271, 281, 290, 309, 322, 335, 353
Overlay, 71 Text Results, 26, 28, 52, 74
Report, 71 Bayes Analyze, 176
Residual, 71
Stacked, 71 Widgets
Trace, 71 Analyze Image Pixel Package
Vertical, 71 Build, 411
File, 28, 80 Find Outliers, 411
Fortran/C Models, 93, 330 Get Statistics, 413
Image, 27, 59, 415 System, 411
Autoset Grayscale, 61 User, 411
Copy Selected, 62 Analyze Image Pixel Unique Package
Delete All, 61 Build, 423
Delete Selected, 61 Find Outliers, 423
Display Full, 61 Get Statistics, 425
Element Selection, 60 System, 423
Export, 62 User, 423
Get Statistics, 64, 65 Ascii Data Viewer
Get Threshold Statistics, 65 Delete, 53
Grayscale, 63 Left-mouse, 53
Image Selection, 60 Right-mouse, 53
List, 59 Bayes Analyze Package
Load Selected Pixels, 61 By, 158, 176
Max, 64 First Point, 163
Mean, 64 From, 158, 176
Min, 64 Imag Offset, 163
Right Click, 61 Mark, 159
RMS, 64 Max New Res, 157
Save Displayed, 62 New, 159
Save Statistics, 65 Noise, 158
Sdev, 64 Phase, 157
Set Image Area, 62 Primary, 158
Show Histogram, 61 Real Offset, 163
Show Info, 62 Remove, 159
Slice, 62 Remove All, 159
Slice Selection, 60 Reset, 159, 193
Statistics, 60 Restore, 159
Value, 64 Save, 159
View Selected Pixels, 61 Secondary, 159
Viewer Settings, 62 Shim Order, 157, 163
Viewing, 62 Signal, 158
X Pos, 64 To, 158, 176
Y Pos, 64 Bayes Find Resonances Package
Plot Results, 28, 71 Build FID Model, 240, 241, 246
Prior, 27, 65 Constant, 239, 242
INDEX 499

First Trace, 239 Enter Ascii Model Selection Package

Last Trace, 239 Find Outliers, 341
Model Fid Number, 241 System, 341
Phase Model, 239, 242 User, 341
Bayes Metabolite Package Errors In Variables Package
Fid Model, 221 Given Errors In, 303
Fid Model Viewer, 221 Order, 303
Load System Metabolite File, 219 Fid Data Viewer
Load System Resonance File, 221 Autoscale, 56
Load User Metabolite File, 219 Clear Cursors, 56
Load User Resonance File, 221 Cursor A, 56
Shift Left, 221, 222 Cursor B, 56
Shift Right, 221, 222 Delta, 56
Bayes Test Data Package Display Type, 56
# Images, 427 Expand, 56
# Slices, 427 Full, 56
Abscissa, 427 Get Peak, 56
ArrayDim, 427 Left-mouse, 56
Build, 427 Options, 57, 59
Get Job, 428 Right-mouse, 56
Max Value, 427 Trace, 70
Noise SD, 427 Fortran/C Model Viewer
Pe, 427 Abscissa Spinner, 93
Ro, 427 Add Prior, 96
Run, 428 Allow/Disallow Editing, 97
Set (server), 428 Cancel and Exit, 96
Status, 428 Changing Models, 94
System, 427 Code, 93, 94
User, 427 Compile Results, 97
Big Magnetization Transfer Package Compiling, 96
Find Outliers, 259 Create/Edit Model, 93
Big Peak/Little Peak Package Data Columns Spinner, 93
Metabolite, 207 Derived, 96
Solvent, 207 Edit/Create New Model, 93, 94
Diffusion Tensor Package High, 97
Abscissa Options, 248 Low, 97
Find Outliers, 247 Mean, 97
Include Constant, 247, 248, 255 Model, 96
Tensor Number, 247, 248, 255 Model Vectors, 93
Use b Matrix, 255 Name (parameter), 97
Use b Vectors, 254, 255 Order, 97
Use g Vectors, 254 Parameter Type, 97
Enter Ascii Model Package Parameters button, 93, 94, 96
Find Outliers, 329 Prior Type, 97
System, 329 Priors, 96
User, 329 Remove All (priors), 96
500 INDEX

Remove Prior, 96 Inversion Recovery Package

Remove Selected Model, 93 Find Outliers, 151
Save and Load, 96 Kernel Density Function Package
Standard Deviation, 97 Kernel Type, 364
Given Exponential Package Output Size, 364
Constant, 137, 139 Linear Phasing Package
Find Outliers, 137 cf, 403
Order, 137, 139 Display, 403
Given Polynomial Order Package Display Array Element, 403
Set Order, 285 fn, 403
Global fn1, 403
Bayes Find Outliers, 27 Image Type, 402
Cancel, 26, 51 Load An Image, 402
Edit Servers, 26 np, 403
Get Job, 26, 51, 137, 143, 151, 155, 209, nv, 403
221, 241, 247, 259, 267, 277, 285, 293, Process, 403
305, 311, 331, 339, 343, 357, 364, 375, Magnetization Transfer Kinetics Package
413, 417, 425, 428 Load, 275, 281
Reset, 27 Set, 275
Restore Analysis, 22 Uncertainty, 275
Run, 26, 51, 137, 143, 151, 155, 207, 221, Magnetization Transfer Package
241, 247, 248, 259, 267, 277, 285, 293, Find Outliers, 265
305, 311, 329, 337, 343, 357, 364, 373, MaxEnt Density Function Estimation Pack-
413, 415, 425, 428 age
Save, 27 Histogram Size, 373
Set (server), 26, 52, 137, 143, 151, 155, Order, 373
207, 221, 239, 247, 259, 265, 277, 285, Non-Linear Phasing Package
293, 305, 311, 329, 337, 343, 355, 364, Process, 409
373, 413, 415, 425, 428 Write Ascii images, 409
Status, 26, 52, 137, 143, 151, 155, 207, Write imaginary images, 409
221, 241, 247, 259, 267, 277, 285, 293, Prior Viewer
305, 311, 329, 337, 343, 355, 364, 373, High, 65
413, 415, 425, 428 Low, 65
Image Model Selection Package Mean, 65
System, 415 Prior Type, 67
User, 415 Server
Image Viewer Edit, 52
Element Number, 62 Name, 26, 52, 52
Get Statistics, 64 Set (server), 48
Get Threshold Statistics, 65 Setup, 48, 52
Grayscale, 63 Test Ascii Model Package
Save Statistics, 65 Find Outliers, 339
Slice Number, 62 System, 337
Value, 64 User, 337
X Pos, 64 Text Results Viewer
Y Pos, 64 Copy, 74
INDEX 501

Down arrow, 74
Enable Editing, 74
Print, 74
Save (a copy), 74
Save As, 74
Settings, 74
Up arrow, 74
Unknown Number of Exponentials Package
Constant, 143
Find Outliers, 143
Order, 143
Unknown Polynomial Order Package
Set Order, 293, 294
Unknown Order, 293, 294
WorkDir
Creating, 22, 33, 46
Deleting, 22, 33, 46
List, 24, 46
Loading, 46
Name, 46
Popup, 47