]> Creatis software - clitk.git/blob - registration/clitkDemonsDeformableRegistration.ggo
Added more options to clitkImageUncertainty, default should be identical
[clitk.git] / registration / clitkDemonsDeformableRegistration.ggo
1 #File clitkDemonsDeformableRegistration.ggo
2 #Author: Jef Vandemeulebroucke <jefvdmb@gmail.com>
3 #Date : Tue 13 Februari 2009 16.35 
4
5 package "clitk"
6 version "Apply Demons registration between (2D or 3D) images..."
7
8
9 option "config"         -       "Config file"                   string          no
10
11
12 section "Run Time"
13
14 option "verbose"        v       "Verbose"                       flag            off
15 option "threads"        -       "Number of threads to use for intensive algorithms (default=min(cores,8))"      int      no
16 option "debug"          -       "Give debug info"               flag            off
17
18
19 section "Input"
20
21 option "reference"      r       "Input reference image"                 string          yes
22 option "target"         t       "Input target image"                    string          yes
23 option "init"           -       "Input initial deformation field"       string          no
24
25 section "Output"
26
27 option "vf"             -       "Result DVF"                            string          yes
28 option "output"         o       "Deformed target image"                 string          yes
29 option "before"         -       "Difference image before "              string          no
30 option "after"          -       "Difference image after "               string          no
31
32 section "Demons"
33
34 option "demons"         -       "Type: 0=normal, 1=symm, 2=fast symm, 3=diffeomorphic"          int             no      default="3"
35 option "levels"         -       "Number of resolution levels"                                   int             no      default="1"     
36 option "maxIter"        -       "Maximum number of iterations at each resolution level"         int             no      multiple default="50"
37 option "maxRMSError"    -       "Maximum RMS error at each resolution level"                    double          no      multiple default="1"    
38 option "stop"           -       "Maximum oscillations at each resolution level (-1=unset)"      int             no      multiple default="-1"                                   
39 option "sd"             -       "SD (in mm) for smoothing in each dimension"                    double          no      multiple default="2.0"
40 option "maxStep"        -       "2,3: Maximum step size (mm)"                                   double          no      default="2"     
41 option "scaleSD"        -       "Scale SD to coarse resolution levels"                          flag            off     
42 option "scaleStep"      -       "2,3: Scale maximum step size to coarse resolution levels"      flag            off     
43 option "fluid"          -       "Smooth update field instead of deformation field"              flag            off     
44 option "spacing"        -       "Use image spacing for derivatives (non-isotropic voxels)"      flag            off
45 option "intThreshold"   -       "0,1,2: Intensity threshold to consider intensity equal"        double          no      default="0.001" 
46 option "movGrad"        -       "1: Use moving image gradient"                                  flag            off     
47 option "gradType"       -       "2,3: 0=Symmetric, 1=fixed, 2=warpedMoving, 3=mappedMoving"     int             no      default="0"     
48 option "firstOrder"     -       "3: Use first order approx for exponential"                     flag            off