1:orphan: 2 3.. Auto-generated by help-rst from "mirtk deform-mesh -h" output 4 5deform-mesh 6=========== 7 8.. program:: deform-mesh 9 10 11Synopsis 12-------- 13 14:: 15 16 deform-mesh <input> <output> [options] 17 18 19Description 20----------- 21 22.. include:: _descriptions/deform-mesh.rst 23 24 25 26Input options 27------------- 28 29.. option:: -initial <file> 30 31 Point set used to initialize the deformed output mesh. Usually the output of a 32 previous optimization with possibly saved node status (see :option:`-save-status`). 33 (default: input) 34 35.. option:: -dof <type> [<dx> [<dy> <dz>]] 36 37 Optimize spatial transformation of named <type> to deform the mesh points. 38 The optional <dx>, <dy>, and <dz> arguments specify the control point spacing 39 of free-form deformation (FFD) transformations. Common transformation types are: 40 41 - ``FFD``: Cubic B-spline FFD. 42 - ``SVFFD``: Stationary velocity (SV) cubic B-spline FFD. 43 44.. option:: -image <file> 45 46 Intensity image on which external forces are based. (default: none) 47 48.. option:: -distance-image, -dmap <file> 49 50 Euclidean distance image on which implicit surface forces are based. (default: none) 51 52.. option:: -distance-offset, -dmap-offset <value> 53 54 Implicit surface isovalue of :option:`-distance-image`. (default: 0) 55 56.. option:: -mask <file> 57 58 Mask defining region in which external forces are non-zero. (default: none) 59 60.. option:: -padding <value> 61 62 Padding/Background value of input :option:`-image`. (default: none) 63 64.. option:: -inflate-brain 65 66 Set default parameters of cortical surface inflation process equivalent 67 to FreeSurfer's mris_inflate command. 68 69 70Optimization options 71-------------------- 72 73.. option:: -optimizer <name> 74 75 Optimization method used to minimize the energy of the deformable surface model: 76 77 - ``EulerMethod``: Forward Euler integration (default) 78 - ``EulerMethodWithDamping``: Forward Euler integration with momentum. 79 - ``EulerMethodWithMomentum``: Forward Euler integration with momentum. 80 - ``GradientDescent``: Gradient descent optimizer. 81 - ``ConjugateGradientDescent``: Conjugate gradient descent. 82 83.. option:: -line-search, -linesearch <name> 84 85 Line search method used by gradient descent optimizers: 86 87 - ``Adaptive``: Line search with adaptive step length. (default) 88 - ``Brent``: Brent's line search method. 89 90.. option:: -damping <value> 91 92 Damping ratio used by Euler method with momentum modelling the effect 93 of dissipation of kinetic energy. 94 95.. option:: -momentum <value> 96 97 Momentum of Euler method with momentum, i.e., :math:`1 - damping` (see :option:`-damping`) 98 99.. option:: -mass <value> 100 101 Node mass used by Euler methods with momentum. (default: 1) 102 103.. option:: -levels <max> | <min> <max> 104 105 Perform optimization on starting at level <max> until level <min> (> 0). 106 When only the <max> level argument is given, the <min> level is set to 1. 107 On each level, the node forces are averaged :math:`2^{level-1}` times which 108 is similar to computing the forces on a coarser mesh. See :option:`-force-averaging`. (default: 0 0) 109 110.. option:: -force-averaging <n>... 111 112 Number of force averaging steps. (default: 0) 113 Cannot be combined with :option:`-magnitude-averaging`. 114 115.. option:: -magnitude-averaging <n>... 116 117 Number of force magnitude averaging steps. (default: 0) 118 Cannot be combined with :option:`-force-averaging`. 119 120.. option:: -distance-averaging <n>... 121 122 Number of :option:`-distance` force averaging steps. (default: 0) 123 124.. option:: -steps, -max-steps, -iterations, -max-iterations <n>... 125 126 Maximum number of iterations. (default: 100) 127 128.. option:: -step, -dt <value>... 129 130 Length of integration/gradient steps. (default: 1) 131 132.. option:: -max-dx, -maxdx, -dx <value>... 133 134 Maximum displacement of a node at each iteration. By default, the node displacements 135 are normalized by the maximum node displacement. When this option is used, the node 136 displacements are clamped to the specified maximum length instead. (default: :option:`-step`) 137 138.. option:: -max-displacement <value> 139 140 Maximum distance from input surface. (default: +inf) 141 142.. option:: -remesh <n> 143 144 Remesh surface mesh every n-th iteration. (default: 0) 145 146.. option:: -remesh-adaptively 147 148 Remesh surface mesh using an adaptive edge length interval based on local curvature 149 of the deformed surface mesh or input implicit surface (:option:`-distance-image`). 150 151.. option:: -triangle-inversion, -notriangle-inversion 152 153 Whether to allow inversion of pair of triangles during surface remeshing. (default: on) 154 155.. option:: -min-edgelength <value>... 156 157 Minimum edge length used for local adaptive remeshing. (default: -1) 158 159.. option:: -max-edgelength <value>... 160 161 Maximum edge length used for local adaptive remeshing. (default: -1) 162 163.. option:: -min-angle <degrees>... 164 165 Minimum angle between edge node normals for an edge be excluded from collapsing during 166 iterative :option:`-remesh` operations. (default: 180) 167 168.. option:: -max-angle <degrees>... 169 170 Maximum angle between edge node normals for an edge be excluded from splitting during 171 iterative :option:`-remesh` operations. (default: 180) 172 173.. option:: -lowpass <n> 174 175 Low-pass filter surface mesh every n-th iteration. (default: 0) 176 177.. option:: -lowpass-iterations <n> 178 179 Number of :option:`-lowpass` filter iterations. (default: 100) 180 181.. option:: -lowpass-band <band> 182 183 Low-pass filtering band argument, usually in the range [0, 2]. (default: 0.75) 184 185.. option:: -nointersection 186 187 Hard non-self-intersection constraint for surface meshes. (default: off) 188 189.. option:: -mind, -min-distance <value> 190 191 Minimum distance to other triangles in front of a given triangle. 192 193.. option:: -minw, -min-width <value> 194 195 Minimum distance to other triangles in the back of a given triangle. 196 197.. option:: -max-collision-angle <degrees> 198 199 Maximum angle between vector connecting centers of nearby triangles and the face normal 200 of the reference triangle for a collision to be detected. When the triangles are within 201 the same flat neighborhood of the surface mesh, this angle will be close to 90 degrees. 202 This parameter reduces false collision detection between neighboring triangles. (default: 45) 203 204.. option:: -fast-collision-test 205 206 Use fast approximate triangle-triangle collision test based on distance of their centers only. (default: off) 207 208.. option:: -reset-status 209 210 Set status of all mesh nodes to active again after each level (see :option:`-levels`). (default: off) 211 212 213Deformable model options 214------------------------ 215 216.. option:: -neighborhood <n> 217 218 Size of node neighborhoods used by internal force terms that consider more 219 than only the adjacent nodes, but also up to n-connected nodes. (default: 2) 220 221.. option:: -distance <w> 222 223 Weight of implicit surface distance. (default: 0) 224 225.. option:: -distance-measure <name> 226 227 Implicit surface distance measure used by :option:`-distance`: 228 229 - ``minimum``: Minimum surface distance (see :option:`-distance-image`, default) 230 - ``normal``: Estimate distance by casting rays along normal direction. 231 232.. option:: -balloon-inflation, -balloon <w> 233 234 Weight of inflation force based on local intensity statistics. (default: 0) 235 236.. option:: -balloon-deflation <w> 237 238 Weight of deflation force based on local intensity statistics. (default: 0) 239 240.. option:: -balloon-min <intensity> 241 242 Global lower intensity threshold for :option:`-balloon-inflation` or :option:`-balloon-deflation`. (default: -inf) 243 244.. option:: -balloon-max <intensity> 245 246 Global upper intensity threshold for :option:`-balloon-inflation` or :option:`-balloon-deflation`. (default: +inf) 247 248.. option:: -balloon-range <min> <max> 249 250 Global intensity thresholds for :option:`-balloon-inflation` or :option:`-balloon-deflation`. (default: [-inf +inf]) 251 252.. option:: -balloon-radius <r> 253 254 Radius for local intensity statistics of :option:`-balloon-inflation` or :option:`-balloon-deflation`. (default: 7 times voxel size) 255 256.. option:: -balloon-sigma <sigma> 257 258 Local intensity standard deviation scaling factor of :option:`-balloon-inflation` or :option:`-balloon-deflation`. (default: 5) 259 260.. option:: -balloon-mask <file> 261 262 Image mask used for local intensity statistics for :option:`-balloon-inflation` or :option:`-balloon-deflation`. 263 (default: interior of deformed surface) 264 265.. option:: -edges <w> 266 267 Weight of image edge force. (default: 0) 268 269.. option:: -edge-distance <w> 270 271 Weight of closest image edge distance force. (default: 0) 272 273.. option:: -inflation <w> 274 275 Weight of surface inflation force used for cortical surface inflation. (default: 0) 276 277.. option:: -bending-energy <w> 278 279 Weight of bending energy of :option:`-dof` transformation. (default: 0) 280 281.. option:: -spring <w> 282 283 Weight of internal spring force. (default: 0) 284 285.. option:: -normal-spring, -nspring <w> 286 287 Weight of internal spring force in normal direction. (default: 0) 288 289.. option:: -tangential-spring, -tspring <w> 290 291 Weight of internal spring force in tangent plane. (default: 0) 292 293.. option:: -normalized-spring <w> 294 295 Weight of internal spring force normalized w.r.t. force in normal direction. (default: 0) 296 297.. option:: -curvature <w> 298 299 Weight of surface curvature. (default: 0) 300 301.. option:: -quadratic-curvature, -qcurvature <w> 302 303 Weight of surface curvature estimated by quadratic fit of node neighbor to tangent plane distance. (default: 0) 304 305.. option:: -distant-quadratic-curvature, -distant-qcurvature <w> 306 307 Weight of :option:`-quadratic-curvature` proportional to the :option:`-distance` magnitude. (default: 0) 308 309.. option:: -mean-curvature, -mcurvature <w> 310 311 Weight of mean curvature constraint. (default: 0) 312 313.. option:: -distant-mean-curvature, -distant-mcurvature <w> 314 315 Weight of :option:`-mean-curvature` proportional to the :option:`-distance` magnitude. (default: 0) 316 317.. option:: -gauss-curvature, -gcurvature <w> 318 319 Weight of Gauss curvature constraint. (default: 0) 320 321.. option:: -distant-gauss-curvature, -distant-gcurvature <w> 322 323 Weight of :option:`-gauss-curvature` proportional to the :option:`-distance` magnitude. (default: 0) 324 325.. option:: -distortion <w> 326 327 Weight of metric distortion. 328 329.. option:: -stretching <w> 330 331 Weight of spring force based on difference of neighbor distance compared to 332 initial distance. (default: 0) 333 334.. option:: -repulsion <w> 335 336 Weight of node repulsion force. (default: 0) 337 338.. option:: -repulsion-radius <r> 339 340 Radius of node repulsion force. (default: average edge length) 341 342.. option:: -repulsion-distance <r> 343 344 Frontface radius of node repulsion force. (default: average edge length) 345 346.. option:: -repulsion-width <r> 347 348 Backface radius of node repulsion force. (default: average edge length) 349 350.. option:: -collision <w> 351 352 Weight of triangle repulsion force. 353 354.. option:: -normal <w> 355 356 Constant force along outwards normal direction (positive weight) 357 or inwards normal direction (negative weight). 358 359 360Stopping criterion options 361-------------------------- 362 363.. option:: -extrinsic-energy 364 365 Consider only sum of external energy terms as total energy value of deformable model functional. 366 Internal forces still contribute to the gradient of the functional, but are excluded from the 367 energy function value (see :option:`-epsilon` and :option:`-min-energy`). (default: off) 368 369.. option:: -epsilon <value> 370 371 Minimum change of deformable surface energy convergence criterion. 372 373.. option:: -delta <value>... 374 375 Minimum maximum node displacement or :option:`-dof` parameter value. (default: 1e-6) 376 377.. option:: -min-energy <value> 378 379 Target deformable surface energy value. (default: 0) 380 381.. option:: -min-active <ratio>... 382 383 Minimum ratio of active nodes in [0, 1]. (default: 0) 384 385.. option:: -inflation-error <threshold> 386 387 Threshold of surface inflation RMS measure. (default: off) 388 389 390Output options 391-------------- 392 393.. option:: -track [<name>] 394 395 Record sum of node displacements along normal direction. The integrated 396 displacements are stored in the point data array named "NormalDisplacement" 397 by default or with the specified <name>. (default: off) 398 399.. option:: -track-zero-mean [<name>] 400 401 Same as :option:`-track`, but subtract mean from tracked values. 402 This option is implicit when :option:`-inflate-brain` is given to inflate a cortical 403 brain surface. The default output array name is "SulcalDepth". Otherwise, the default 404 point data array name is "NormalDisplacementZeroMean". (default: off) 405 406.. option:: -track-zero-median [<name>] 407 408 Same as :option:`-track`, but subtract median from tracked values. 409 The default point data array name is "NormalDisplacementZeroMedian". (default: off) 410 411.. option:: -track-unit-variance [<name>] 412 413 Same as :option:`-track`, but divide tracked values by their standard deviation. 414 The default point data array name is "NormalDisplacementUnitVariance". (default: off) 415 416.. option:: -track-zvalues [<name>] 417 418 Same as :option:`-track`, but subtract mean from tracked values and divide by standard deviation. 419 The resulting values are the Z-score normalized standard scores of the tracked displacements. 420 The default point data array name is "NormalDisplacementZValues". (default: off) 421 422.. option:: -track-zero-median-zvalues [<name>] 423 424 Same as :option:`-track`, but subtract median from tracked values and divide by standard deviation. 425 It can be used with :option:`-inflate-brain` to obtain a normalized curvature measure. 426 The default point data array name is "NormalDisplacementZeroMedianZValues". (default: off) 427 428.. option:: -track-without-momentum 429 430 When tracking the total displacement of a node in normal direction using the EulerMethodWithMomentum 431 :option:`-optimizer` as used in particular by :option:`-inflate-brain`, exclude the momentum from the. 432 tracked displacement. This is idential to FreeSurfer's mrisTrackTotalDisplacement used for the curvature 433 output of mris_inflate. The correct curvature value is, however, obtained by including the momentum 434 component as it integrates the actual amount by which each node is displaced during the Euler steps. 435 Not using this option corresponds to the mrisTrackTotalDisplacementNew function. (default: off) 436 437.. option:: -notrack 438 439 Do not track node displacements along normal direction. 440 441.. option:: -center-output 442 443 Center output mesh such that center is at origin. (default: off) 444 445.. option:: -match-area 446 447 Scale output mesh by ratio of input and output surface area. (default: off) 448 449.. option:: -match-sampling 450 451 Resample output mesh at corresponding positions of input mesh. 452 This option is only useful in conjunction with :option:`-remesh`. (default: off) 453 454.. option:: -save-status 455 456 Save node status (active/passive) to output file. (default: off) 457 458.. option:: -ascii | -nobinary 459 460 Write legacy VTK in ASCII format. (default: off) 461 462.. option:: -binary | -noascii 463 464 Write legacy VTK in binary format. (default: on) 465 466.. option:: -compress, -nocompress 467 468 Write XML VTK file with or without compression. (default: on) 469 470.. option:: -debug-prefix <prefix> 471 472 File name prefix for :option:`-debug` output. (default: deform_mesh\_) 473 474.. option:: -debug-interval <n> 475 476 Write :option:`-debug` output every n-th iteration. (default: 10) 477 478.. option:: -level-prefix, -nolevel-prefix 479 480 Write :option:`-debug` output without level prefix in file names. (default: on) 481 482 483Advanced options 484---------------- 485 486.. option:: -par <name> <value> 487 488 Advanced option to set surface model or optimizer parameter. 489 490 491Standard options 492---------------- 493 494.. option:: -v, -verbose [n] 495 496 Increase/Set verbosity of output messages. (default: 1) 497 498.. option:: -debug [level] 499 500 Increase/Set debug level for output of intermediate results. (default: 0) 501 502.. option:: -version [major.minor] 503 504 Print version and exit or set version to emulate. 505 506.. option:: -revision 507 508 Print revision (or version) number only and exit. 509 510.. option:: -h, -help 511 512 Print help and exit. 513 514 515Terminal options 516---------------- 517 518.. option:: -color, -nocolor 519 520 Enable/disable colored output. (default: off) 521 522 523Parallelization options 524----------------------- 525 526.. option:: -threads <n> 527 528 Use maximal <n> threads for parallel execution. (default: automatic) 529