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[clitk.git] / registration / clitkCalculateTRE.ggo

diff --git a/registration/clitkCalculateTRE.ggo b/registration/clitkCalculateTRE.ggo
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+#File clitkCalculateTRE.ggo
+Package "clitkCalculateTRE"
+version "1.0"
+purpose "Calculate TRE: give a reference point list and 1 or more target point lists. In case of the latter, the number of DVF (or the size of the 4th D) given should match the number of lists. Use --shipFirst to skip the first phase of a 4D DVF. General summarizes for all points (mean, SD, max) in magnitude and par component. Tre and warp gives all values for all points. "
+
+option "config"                -       "Config file"                     string        no
+option "verbose"       v       "Verbose"                         flag          off
+
+
+section "Input"
+
+option "ref"                   -       "List of points in reference"           string          yes                     
+option "input"         i       "Lists of points in targets"            string          multiple        yes
+option "vf"                    -       "Input deformation fields"              string          multiple        yes
+option "skip"          -       "Skip a phase of a 4D DVF"              int             no      
+
+section "Interpolation"
+
+option "interpVF"      -       "Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT"      int     no  default="1"
+option "interpVFOrder" -       "Order if BLUT or BSpline (0-5)"                        int     no  default="3"
+option "interpVFSF"    -       "Sampling factor if BLUT"                               int     no  default="20"
+
+
+section "Output"
+
+option "general"               -       "Summarized TRE values (mean, SD, max)" string          no      
+option "original"              -       "Original distances: base filename"     string          no      
+option "originalMag"           -       "Original magnitude of distances: base filename"        string          no      
+option "displacement"          -       "Estmated displacements: base filename" string          no      
+option "displacementMag"       -       "Estimated magnitude displacements: base filename"      string          no
+option "tre"                   -       "All TRE values: base filename"         string          no      
+option "treMag"                        -       "All TRE magnitude values: base filename"               string          no      
+option "warp"                  -       "All warped points: base filename"      string          no