NAME
   caret_command   v5.510 (Jun 15 2007)

   For usage information run with "-help" or "-help-full".

NOTE ABOUT PARAMETERS
   Parameters beginning with "b-" are boolean parameters and should
   have a value of either "true" or "false".

   Parameters beginning with "f-" are floating point numbers.

   Parameters beginning with "i-" are integer parameters.

   Parameters containing "name" are names of files.

   All other parameters are descibed in the usage information.

   The input and output file names may be the same.

NOTE ABOUT OUTPUT VOLUME 
   The output volume file may be named the same as the input volume file.
   Volumes are typically written in LPI orientation.

   If desired, a label for the output volume may be prepended to the output
   volume name with the label and file name separated by ":::".
   The label may not contain any spaces.
   Example:      the_label:::the_file_name.HEAD

   The type of output volume is determined by the output file's extension.
   Extension   Type of Volume Written
   
   .hdr        Analyze (SPM/MEDx)
   .HEAD       AFNI
   .ifh        Washington University Format
   .mnc        MINC
   .nii        NIFTI
   
DESCRIPTION OF OPERATIONS

   HELP
      caret_command -help
         Displays brief description of all available operations for this program.

      caret_command -help-full
         Displays full description of all available operations for this program.

  For best results, run this program from the directory containing the files.


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   CARET DATA FILE COMPARISON
      caret_command -caret-data-file-compare <file-1-name> <file-2-name> [f-tolerance]

      Compare two Caret data files of the same type.

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   DEFORMATION MAP FILE SOURCE/TARGET PATH UPDATE
      caret_command -def-map-path \ 
         <deformation-map-file> <source-path> <target-path>
         
      Update the source (individual) and target (atlas) paths in
      a deformation map file.


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   FOCI TABLE EXTRACTION FROM XHTML
      caret_command -foci-xhtml-table <xhtml-file> <csv-file>

      Read an XHTML file, extract the tables, and place 
      the tables into a Comma Separated Value File.

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   IMAGE COMPARE
      caret_command -image-compare \
         <image-file-name-1> <image-file-name-2> 

      Compare two image files to see if the pixels are exactly the same.

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   IMAGE VIEW
      caret_command -image-view <image-file-name> 

      View an image file.

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   METRIC/SHAPE FILE COMPOSITE ALL COLUMNS
      caret_command -metric-or-shape-composite \ 
         <output-metric-or-shape-file> <input-metric-or-shape files...>
         
      Concatenate all columns from the input metric/shape files and place
      them into the output metric/shape file.


------------------------------------------------------------------------------
   METRIC/SHAPE FILE COMPOSITE ALL COLUMNS
      caret_command -metric-or-shape-composite-named-column \ 
         <name-of-column-that-is-case-sensitive> \
         <output-metric-or-shape-file> <input-metric-or-shape files...>
         
      Concatenate selected columns from the input metric/shape files and place
      them into the output metric/shape file.  Only those columns that match
      the specified column name are appended.  If there are more than one
      columns with the name in the file, ALL will be appended.


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   METRIC/SHAPE FILE COPY COLUMNS TO NEW FILE
      caret_command -metric-or-shape-copy-columns-to-new-file \ 
         <input-metric-file> <output-metric-file> <columns-to-copy>
         
      Copy columns from a metric file into a new metric file.
      
      The <columns-to-copy> specifies the columns that are to be copied
      from the input file.  You may specify single columns or a range of
      columns separated by a comma.  Column numbers start at one.
      Example:
            1,3-5,7-9,12
         This above specifies that columns 1, 3, 4, 5, 7, 8, 9, and 12
         will be copied to the new file.


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   METRIC/SHAPE IN GROUP DIFFERENCE
     caret_command -metric-or-shape-in-group-diff \ 
        <input-metric-or-shape-file> <output-metric-or-shape-file> \
        <b-abs-value-flag> 
        
     Compute the difference between each column in the metric/shape file.
     and all other columns in the metric shape file.  The number of columns
     in the output metric file is [N! / (K! * (N - K)!)] where N is the.
     number of columns in the input metric/shape file and K is 2.
     
     The abs-value-flag is either "true" or "false".  If the 
     abs-value-flag is true, the output is all absolute values of
     the differences.


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   METRIC/SHAPE STATISTICS COORDINATE DIFFERENCE
     caret_command -metric-or-shape-stat-coord-diff \ 
        <mode>  \
        <fiducial-coord-file>  \
        <open-topo-file> \
        <distortion-metric-shape-file>  \
        <distortion-column-number> \
        <output-file-names-prefix> \
        <i-iterations>  \
        <f-threshold>  \
        <f-p-value>  \
        <i-number-of-threads> \
        -groupA <one-or-more-coord-files-from-group-A> \
        -groupB <one-or-more-coord-files-from-group-B> 
        
     Find clusters in groups of coordinate files.
     
     mode is one of:
        COORD_DIFF - search for clusters in coordinate difference.
        TMAP_DIFF  - search for clusters using T-Test of coordinate difference.
     
     The distortion column number starts at 1.
     
     Number of threads is the number of concurrent processes run
     during the cluster search of the shuffled metric/shape file.
     Use "1" if you are running on a single processor system.
     Users on systems with multiple processors or multi-core systems
     should set the number of threads to the number of processors
     and/or cores to reduce execution time.


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   METRIC/SHAPE FILE CORRELATION COEFFICIENT MAP
      caret_command -metric-or-shape-correlation-map \ 
         <input-metric-or-shape-file-A> \ 
         <input-metric-or-shape file-B> \
         <output-metric-or-shape-file>  
         
      For each node, compute a correlation coefficient from the node's values
      in the two input metric files.  The two input files must have the same
      number of columns and column 'x' in the two files should contain data
      for the same subject.

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   METRIC/SHAPE FILE INFORMATION
      caret_command -metric-or-shape-file-info \ 
         <metric-or-shape-file>  
         
      Print information about contents of a metric or shape file.

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   METRIC/SHAPE FILE SET COLUMN NAME
      caret_command -metric-or-shape-set-column-name \ 
         <column-number> \ 
         <new-column-name> \
         <metric-or-shape-file>  
         
      Set the name of a column in the metric/shape file.
         
      Note: Column numbers start at one.

------------------------------------------------------------------------------
   METRIC/SHAPE FILE SET COLUMN TO VALUE
      caret_command -metric-or-shape-set-column-to-value \ 
         <column-number> \ 
         <new-value> \
         <metric-or-shape-file>  
         
      Set the value for all nodes in a column.
         
      Note: Column numbers start at one.

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   METRIC/SHAPE FILE CREATE
      caret_command -metric-or-shape-create \ 
         <number-of-nodes> \ 
         <number-of-columns> \
         <output-metric-or-shape-file>  
         
      Create a metric or shape file with the specified number of nodes and
      columns.  All values are initialized to zero.

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   METRIC/SHAPE STATISTICS ONE-WAY ANOVA
     caret_command -metric-or-shape-stat-anova-one-way \ 
        <fiducial-coord-file>  \
        <open-topo-file> \
        <distortion-metric-shape-file>  \
        <distortion-column-number> \
        <output-file-names-prefix> \
        <i-iterations>  \
        <f-positive-threshold> \
        <f-p-value> \
        <b-do-fmap-DOF>  \
        <b-do-fmap-pvalue> \
        <number-of-threads> \
        <metric-or-shape-files> 
        
     Perform a one-way analysis of variance on the input metric files. 
     There must be at least two "metric-or-shape-files" and each of the
     metric or shape files contains all of the subjects for one factor level.
     
     The distortion column number starts at 1.
     
     Number of threads is the number of concurrent processes run
     during the cluster search of the shuffled metric/shape file.
     Use "1" if you are running on a single processor system.
     Users on systems with multiple processors or multi-core systems
     should set the number of threads to the number of processors
     and/or cores to reduce execution time.


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   METRIC/SHAPE STATISTICS INTERHEMISPHERIC CLUSTERS
     caret_command -metric-or-shape-stat-interhemispheric-clusters \ 
        <metric-or-shape-file-right-A>  \
        <metric-or-shape-file-right-B> \
        <metric-or-shape-file-left-A>  \
        <metric-or-shape-file-left-B> \
        <fiducial-coord-file>  \
        <open-topo-file> \
        <distortion-metric-shape-file>  \
        <distortion-column-number> \
        <output-file-names-prefix> \
        <i-iterations-shuffled-tmap>  \
        <i-iterations-right-left-shuffled-tmap> \
        <f-negative-threshold>  \
        <f-positive-threshold>  \
        <f-p-value> \
        <i-variance-smoothing-iterations>  \
        <f-variance-smoothing-strength> \
        <b-do-tmap-DOF>  \
        <b-do-tmap-pvalue> \
        <number-of-threads> 
        
     Search for interhemispheric clusters.
     
     The distortion column number starts at 1.
     
     Number of threads is the number of concurrent processes run
     during the cluster search of the shuffled metric/shape file.
     Use "1" if you are running on a single processor system.
     Users on systems with multiple processors or multi-core systems
     should set the number of threads to the number of processors
     and/or cores to reduce execution time.


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   METRIC/SHAPE STATISTICS KRUSKAL-WALLIS
     caret_command -metric-or-shape-stat-kruskal-wallis \ 
        <fiducial-coord-file>  \
        <open-topo-file> \
        <distortion-metric-shape-file>  \
        <distortion-column-number> \
        <output-file-names-prefix> \
        <i-iterations>  \
        <f-positive-threshold> \
        <f-p-value> \
        <b-do-fmap-DOF>  \
        <b-do-fmap-pvalue> \
        <number-of-threads> \
        <metric-or-shape-files> 
        
     Perform a Kruskal-Wallis Rank Test (essentially a non-parametric
     one-way analysis of variance) on the input metric files. 
     There must be at least two "metric-or-shape-files" and each of the
     metric or shape files contains all of the subjects for one factor level.
     
     The distortion column number starts at 1.
     
     Number of threads is the number of concurrent processes run
     during the cluster search of the shuffled metric/shape file.
     Use "1" if you are running on a single processor system.
     Users on systems with multiple processors or multi-core systems
     should set the number of threads to the number of processors
     and/or cores to reduce execution time.


------------------------------------------------------------------------------
   METRIC/SHAPE STATISTICS ONE SAMPLE T-TEST
     caret_command -metric-or-shape-stat-one-sample-t-test \ 
        <metric-or-shape-file> \
        <fiducial-coord-file>  \
        <open-topo-file> \
        <distortion-metric-shape-file>  \
        <distortion-column-number> \
        <output-file-names-prefix> \
        <f-negative-threshold>  \
        <f-positive-threshold> \
        <f-p-value> \ 
        <i-variance-smoothing-iterations>  \
        <f-variance-smoothing-strength> \
        <i-iterations>  \
        <f-t-test-constant> \
        <number-of-threads> 
        
     Perform a one-sample T-Test on the metric/shape file.
     
     The distortion column number starts at 1.
     
     Number of threads is the number of concurrent processes run
     during the cluster search of the shuffled metric/shape file.
     Use "1" if you are running on a single processor system.
     Users on systems with multiple processors or multi-core systems
     should set the number of threads to the number of processors
     and/or cores to reduce execution time.


------------------------------------------------------------------------------
   METRIC/SHAPE STATISTICS PAIRED T-TEST
     caret_command -metric-or-shape-stat-paired-t-test \ 
        <metric-or-shape-file-A> \
        <metric-or-shape-file-B> \
        <fiducial-coord-file> \
        <open-topo-file> \
        <distortion-metric-shape-file> \
        <distortion-column-number> \
        <output-file-names-prefix> \
        <f-negative-threshold> \
        <f-positive-threshold> \
        <f-p-value> \ 
        <i-variance-smoothing-iterations> \
        <f-variance-smoothing-strength> \
        <i-iterations> \
        <number-of-threads> \
        
     Perform a paired T-Test on the metric/shape file.
     
     The distortion column number starts at 1.
     
     Number of threads is the number of concurrent processes run
     during the cluster search of the shuffled metric/shape file.
     Use "1" if you are running on a single processor system.
     Users on systems with multiple processors or multi-core systems
     should set the number of threads to the number of processors
     and/or cores to reduce execution time.


------------------------------------------------------------------------------
   METRIC/SHAPE STATISTICS TWO SAMPLE T-TEST and WILCOXON
     caret_command -metric-or-shape-stat-two-sample-t-test \ 
        <data-transform-mode-name>  \
        <variance-mode-name> \ 
        <metric-or-shape-file-A>  \
        <metric-or-shape-file-B> \
        <fiducial-coord-file>  \
        <open-topo-file> \
        <distortion-metric-shape-file>  \
        <distortion-column-number> \
        <output-file-names-prefix> \
        <i-iterations>  \
        <f-negative-threshold>  \
        <f-positive-threshold> \
        <f-p-value> \
        <i-variance-smoothing-iterations>  \
        <f-variance-smoothing-strength> \
        <b-do-tmap-DOF>  \
        <b-do-tmap-pvalue> \
        <number-of-threads> 
        
     Perform a two-sample T-Test or perform a Wilcoxon Rank-Sum of the 
     data and then perform the T-Test.
     
     data-transform-mode-name one of:
        NO_TRANSFORM
        WILCOXON_TRANSFORM  (Wilcoxon Rank-Sum input data then T-Test)
     
     variance-mode-name is one of:
        SIGMA      - Use Donna's SIGMA method
        POOLED     - Use pooled variance in T computation
        UNPOOLED   - Use unpooled variance in T computation
     
     The distortion column number starts at 1.
     
     Number of threads is the number of concurrent processes run
     during the cluster search of the shuffled metric/shape file.
     Use "1" if you are running on a single processor system.
     Users on systems with multiple processors or multi-core systems
     should set the number of threads to the number of processors
     and/or cores to reduce execution time.


------------------------------------------------------------------------------
   METRIC/SHAPE FILE TWIN COMPARISON
     caret_command -metric-or-shape-twin-comparison \ 
     <input-metric-or-shape-file-A> <input-metric-or-shape-file-B> \
     <output-metric-shape-file>

     Metric/Shape File A and Metric/Shape File B contain twin subjects
     such that one of the twins is in File A and its corresonding twin
     is in the same column but in File B.
     The output file contains the twin-paired expected variance,
     the expected variance of all non-twin pairs, and the the difference
     of the two expected variances.


------------------------------------------------------------------------------
   METRIC/SHAPE FILE PAIRED DATA DIFFERENCES
     caret_command -metric-or-shape-twin-paired-data-diffs \ 
     <input-metric-or-shape-file-group-A> <input-metric-or-shape-file-group-B> \
     <directory-for-diffs>
     Compare the two data files, assuming a paired relationship in the
     same column numbers in the two data files, e.g., the first pair of twins
     are both the first column in data file A and data file B, respectively


------------------------------------------------------------------------------
   SHOW SCENE
      caret_command -show-scene \ 
         <spec-file> <scene-file> <i-scene-number> \
         [image-file-name]
         
      Render the images of a scene into an image file.
      Note: The scene numbers start at one.   
         

      NOTE: If the image file name is not specified, the image of the scene
      will be shown in a window on the user's display.

------------------------------------------------------------------------------
   SHOW SURFACE
      caret_command -show-surface \ 
         <topo-file> <coord-file> <view> \
         <i-image-width> <i-image-height> [image-file-name]
         
      Render an image of the surface into an image file or to the user's display.

      view is one of:  
         A    => anterior view
         ALL  => all size views in one image
         D    => dorsal view
         L    => lateral view
         M    => medial view
         P    => posterior view
         V    => ventral view
         

      NOTE: If the image file name is not specified, the image of the surface
      will be shown in a window on the user's display.

------------------------------------------------------------------------------
   SHOW VOLUME
      caret_command -show-volume \ 
         <axis> <slice> <volume-file-name> \
         <i-image-width> <i-image-height> [image-file-name]
         
      Render an image of the surface into an image file or to the user's display.

      axis is one of:  
         X    => x-axis (parasagittal view)
         Y    => y-axis (coronal view)
         Z    => z-axis (horizontal/axial view)
         

      NOTE: If the image file name is not specified, the image of the volume
      will be shown in a window on the user's display.

------------------------------------------------------------------------------
   SPEC FILE ADD
      caret_command -spec-file-add \ 
         <spec-file-name> <spec-file-tag> <data-file-name> \ 
         [data-file-second-name] 
         
      Add a tag to a spec file.
      
      The filename "data-file-name" is added to the spec file using
      the "spec-file-tag".  If a volume file is added, specify the
      header file as "data-file-name" and the data file as
      "data-file-second-name".

      NOTE: The spec file must already exist.

      Valid spec file tags are: 
         TAG                                 DESCRIPTION
         volume_functional_file              Volume - Functional
         volume_paint_file                   Volume - Paint
         volume_prob_atlas_file              Volume - Probabilistic Atlas
         volume_rgb_file                     Volume - RGB
         volume_segmentation_file            Volume - Segmentation
         volume_anatomy_file                 Volume - Anatomy
         volume_vector_file                  Volume - Vector
         CLOSEDtopo_file                     Topology - Closed
         OPENtopo_file                       Topology - Open
         CUTtopo_file                        Topology - Cut
         LOBAR_CUTtopo_file                  Topology - Lobar Cut
         topo_file                           Topology - Unknown
         RAWcoord_file                       Coordinate - Raw
         FIDUCIALcoord_file                  Coordinate - Fiducial
         INFLATEDcoord_file                  Coordinate - Inflated
         VERY_INFLATEDcoord_file             Coordinate - Very Inflated
         SPHERICALcoord_file                 Coordinate - Spherical
         ELLIPSOIDcoord_file                 Coordinate - Ellipsoid
         COMPRESSED_MEDIAL_WALLcoord_file    Coordinate - Compressed Medial Wall
         FLATcoord_file                      Coordinate - Flat
         LOBAR_FLATcoord_file                Coordinate - Lobar Flat
         HULLcoord_file                      Coordinate - Hull
         AVERAGE_FIDUCIALcoord_file          Coordinate - Average Fiducial
         coord_file                          Coordinate - Unknown
         RAWsurface_file                     Surface - Raw
         FIDUCIALsurface_file                Surface - Fiducial
         INFLATEDsurface_file                Surface - Inflated
         VERY_INFLATEDsurface_file           Surface - Very Inflated
         SPHERICALsurface_file               Surface - Spherical
         ELLIPSOIDsurface_file               Surface - Ellipsoid
         COMPRESSED_MEDIAL_WALLsurface_file  Surface - Compressed Medial Wall
         FLATsurface_file                    Surface - Flat
         LOBAR_FLATsurface_file              Surface - Lobar Flat
         HULLsurface_file                    Surface - Hull
         surface_file                        Surface - Unknown
         lat_lon_file                        Latitude/Longitude File
         section_file                        Section File
         scene_file                          Scene File
         image_file                          Image File
         transformation_matrix_file          Transformation Matrix File
         paint_file                          Paint File
         area_color_file                     Area Color File
         RGBpaint_file                       RGB Paint File
         surface_vector_file                 Surface Vector File
         RAWborder_file                      Border File - Raw
         FIDUCIALborder_file                 Border File - Fiducial
         INFLATEDborder_file                 Border File - Inflated
         VERY_INFLATEDborder_file            Border File - Very Inflated
         SPHERICALborder_file                Border File - Spherical
         ELLIPSOIDborder_file                Border File - Ellipsoid
         COMPRESSED_MEDIAL_WALLborder_file   Border File - Comp Med Wall
         FLATborder_file                     Border File - Flat
         LOBAR_FLATborder_file               Border File - Lobar Flat
         HULLborder_file                     Border File - Hull
         VOLUMEborder_file                   Border File - Volume
         border_file                         Border File - Unknown
         border_color_file                   Border Color File
         borderproj_file                     Border Projection File
         momc_template_file                  Momc Template
         momc_template_match_file            Momc Template Match
         palette_file                        Palette File
         topography_file                     Topography File
         cell_file                           Cell File
         cell_color_file                     Cell Color File
         cellproj_file                       Cell Projection File
         volume_cell_file                    Volume Cell File
         contour_file                        Contour File
         contour_cell_file                   Contour Cell File
         contour_cell_color_file             Contour Cell Color File
         atlas_file                          Prog Atlas File
         metric_file                         Metric File
         surface_shape_file                  Surface Shape File
         cocomac_connect_file                CoCoMac File
         areal_estimation_file               Areal Estimation File
         cuts_file                           Cuts File
         foci_file                           Foci File
         foci_color_file                     Foci Color File
         fociproj_file                       Foci Projection File
         volume_foci_file                    Volume Foci File
         params_file                         Params File
         deform_map_file                     Deformation Map File
         deform_field_file                   Deformation Field File
         CEREBRAL_HULLvtk_file               Cerebral Hull File
         vtk_model_file                      VTK Model File
         geodesic_distance_file              Geodesic Distance File
         wustl_region_file                   WUSTL Region File
         transformation_data_file            Transformation Data File
         meta_analysis_file                  Study Meta-Analysis File
         study_metadata_file                 Study Metadata File
         vocabulary_file                     Vocabulary File
         document_file                       Document File
      
------------------------------------------------------------------------------
   SPEC FILE CREATE
      caret_command -spec-file-create \ 
         <species> <subject> <structure> <stereotaxic-space> \ 
         <category> [spec-file-name] 
         
      Create a spec file.
      
      The "spec-file-name" is optional and should only be specified 
      if you must name the spec file.  If the "spec-file-name" is not
      specified, the spec file name will be created using the Caret 
      standard which composes the spec file name using the species,
      subject, and structure.
      
      Note: None of the parameters may contain blank characters (spaces).
      
      Examples of "species" are: 
         Baboon
         Chimpanzee
         Ferret
         Galago
         Gibbon
         Gorilla
         Human
         Macaque
         Mouse
         Orangutan
         Rat
         Other

      Examples of "structure" are: 
         cerebellum
         left
         both
         right

      Examples of "stereotaxic-space" are: 
         Unknown
         Other
         AFNI
         FLIRT
         MACAQUE-F6
         MACAQUE-F99
         MRITOTAL
         SPM
         SPM95
         SPM96
         SPM99
         SPM2
         SPM5
         T88
         711-2B
         711-2B-111
         711-2B-222
         711-2B-333
         711-2C
         711-2C-111
         711-2C-222
         711-2C-333
         711-2O
         711-2O-111
         711-2O-222
         711-2O-333
         711-2Y
         711-2Y-111
         711-2Y-222
         711-2Y-333

      Examples of "category" are: 
         ATLAS
         INDIVIDUAL
         TUTORIAL

------------------------------------------------------------------------------
   STATISTICS UNIT TESTING
      caret_command -statistic-unit-test <b-show-values-flag>

      Perform unit testing on statistics code. 

      <b-show-values-flag> if "true" all test values are shown.  If 
      "false", only errors are displayed.

------------------------------------------------------------------------------
   SURFACE APPLY DEFORMATION MAP
      caret_command -surface-deformation-apply \ 
         <deformation-map-file> <file-type> \
         <input-file>  <output-file> \
         [source-topo-file]  [source-deformed-topo-file] \
         [atlas-topo-file]
         
      Deform a data file.

      Note: "source-topo-file", "source-deformed-topo-file" and 
      "atlas-topo-file" are only required when deforming
      coordinate files.

      "file-type" is one of: 
         AREAL_ESTIMATION
         BORDER_FLAT
         BORDER_PROJECTION
         BORDER_SPHERICAL
         CELL
         CELL_PROJECTION
         COORDINATE
         COORDINATE_FLAT
         FOCI
         FOCI_PROJECTION
         LAT_LON
         METRIC
         PAINT
         PROB_ATLAS
         RGB_PAINT
         SURFACE_SHAPE
         TOPOGRAPHY


------------------------------------------------------------------------------
   SURFACE CREATE AVERAGE
      caret_command -surface-average \ 
         <output-coordinate-file> \ 
         <input-coordinate-file> [additional-input-coordinate-files] \
         [optional-surface-shape-file-name] 
         
      Create an average surface.
      
      Since the type of surface being averaged is unknown, there is 
      no option to update a spec file.  If you wish to update a spec
      file, see the help information for "-spec-file-add".
      
      If a surface shape file name is specified, it will be created
      and contain the coordinate uncertainty.  If a surface shape file
      is specified, its name MUST END WITH ".surface_shape".

------------------------------------------------------------------------------
   SURFACE BORDER EXTREMA
      caret_command -surface-border-extrema \ 
         <input-topo-file> <input-coord-file> <input-border-file> <border-name>
         
      List the extrema for the surface, the extrema for the border, and the 
      difference between the extrema. 


------------------------------------------------------------------------------
   SURFACE BORDER NIBBLER (remove border points within a distance to surface extrema)
      caret_command -surface-border-nibbler \ 
         <input-topo-file> <input-coord-file> <input-border-file> <border-name>
         <output-border-file> <surface-extrema-name-or-node-indicator>
          <surface-extrema-offset-or-node-number> <pos-neg>
         
      Remove points from the named border that are within that are on a . 
      specified side of a surface extrema or node number.
      
      Surface-extrema-name-or-node-indicator is one of "xmin", "xmax", 
      "ymin", "ymax", "zmin", "zmax", "node-x", "node-y", or
      or "node-z".
      
      Surface-extrema-offset-or-node-number is added to the X, Y, or Z of the
       specified surface-extrema or is the number of a node.
      
      <pos-neg> is either "POS" or "NEG" and indicates if border points
      should be removed from the positive or negative side of the surface 
      extrema and offset or node number.
      
      Suppose the surface extrema name/offset/pos-neg are "ymin  20  NEG" 
      and the surface's minimum Y-coordinate is -125.0.   Border points having
      a Y-coordinate less than 105.0 (-125 + 20) are removed.  Changing the
      plus-minus to POS would remove all border points with a Y-coordinate
      greater than 105.0.
      
      Suppose the node indicator/node number/pos-neg are "node-x 25432 POS".
      Any border points with an X-coordinate greater than the X-coordinate of 
      node 25432 are removed.
      
      

------------------------------------------------------------------------------
   SURFACE BORDER PROJECTION
      caret_command -surface-border-projection \ 
         <input-topo-file> <input-coord-file> \
         <input-border-file>  <output-border-projection-file> \
         <output-spec-file>
         
      Project a border file to the surface (coord/topo pair).
      The spec file is optional and, if supplied, the output border 
      projection file will be added to the spec file.


------------------------------------------------------------------------------
   SURFACE BORDER UNPROJECTION
      caret_command -surface-border-unprojection \ 
         <input-coord-file> \
         <input-border-projectionfile>  <output-border-file> \
         <output-spec-file> <spec-file-tag>
         
      Unproject a border projection file to the coordinate file.
      The spec file is optional and, if supplied, the output border file
      will be added to the spec file.

      spec-file-tag should be one of the following border file tags:
         RAWborder_file
         FIDUCIALborder_file
         INFLATEDborder_file
         VERY_INFLATEDborder_file
         SPHERICALborder_file
         ELLIPSOIDborder_file
         COMPRESSED_MEDIAL_WALLborder_file
         FLATborder_file
         LOBAR_FLATborder_file
         border_file


------------------------------------------------------------------------------
   SURFACE BORDER VARIABILITY
      caret_command -surface-border-variability \ 
         <input-border-file> <input-landmark-average-border-file> \
         <output-border-file> \
         
      Resample the input borders so that they have the same number of 
      links as the border with the corresponding name in the input landmark 
      average border file.  In addition, the variability radius for the 
      borders will also be set.

------------------------------------------------------------------------------
   SURFACE CELL PROJECTION
      caret_command -surface-cell-projection \ 
         <input-topo-file> <input-coord-file> \
         <input-cell-file>  <output-cell-projection-file> \
         <b-onto-surface-flag>  <f-onto-surface-above-distance> \
         <output-spec-file>
         
      Project a cell file to the surface (coord/topo pair).
      The spec file is optional and, if supplied, the output cell 
      projection file will be added to the spec file.

      b-onto-surface-flag should be either "true" or "false".  If
      it is true, cells will be projected so that they are 
      f-onto-surface-above-distance units above the surface.  If false
      cells are projected so that they retain their surface offset.


------------------------------------------------------------------------------
   SURFACE CELL UNPROJECTION
      caret_command -surface-cell-unprojection \ 
         <input-topo-file> <input-coord-file> \
         <input-cell-projection-file>  <output-cell-file> \
         <output-spec-file>
         
      Unproject a cell projection file to the coordinate file.
      The spec file is optional and, if supplied, the output cell file
      will be added to the spec file as a fiducial cell file.


------------------------------------------------------------------------------
   SURFACE CROSSOVER CHECK
      caret_command -surface-crossover-check \ 
         <coordinate-file-name> <topology-file-name> 
         
      Perform a crossover check on a surface (coordinate and topology files).
         


------------------------------------------------------------------------------
   SURFACE FLAT MULTIRESOLUTION MORPHING
      caret_command -surface-flat-multi-morph \ 
         <input-spec-file> <input-cut-topo-file>\
         <input-fiducial-coord-file>  <input-flat-coord-file> \
         
      Peform flat multi-resolution morphing (distortion correction).


------------------------------------------------------------------------------
   SURFACE FOCI PROJECTION
      caret_command -surface-foci-projection \ 
         <input-topo-file> <input-coord-file> \
         <input-foci-file>  <output-foci-projection-file> \
         <b-onto-surface-flag>  <f-onto-surface-above-distance> \
         <output-spec-file>
         
      Project a foci file to the surface (coord/topo pair).
      The spec file is optional and, if supplied, the output foci 
      projection file will be added to the spec file.

      b-onto-surface-flag should be either "true" or "false".  If
      it is true, foci will be projected so that they are 
      f-onto-surface-above-distance units above the surface.  If false
      foci are projected so that they retain their surface offset.


------------------------------------------------------------------------------
   SURFACE FOCI UNPROJECTION
      caret_command -surface-foci-unprojection \ 
         <input-topo-file> <input-coord-file> \
         <input-foci-projection-file>  <output-foci-file> \
         <output-spec-file> 
         
      Unproject a foci projection file to the coordinate file.
      The spec file is optional and, if supplied, the output foic file
      will be added to the spec file as a fiducial foci file.


------------------------------------------------------------------------------
   SURFACE GENERATE INFLATED and/or ELLIPSOID
      caret_command -surface-generate \ 
         <input-fiducial-coord-file> <input-closed-topology-file> \ 
         <output-inflated-coord-file> <output-very-inflated-coord-file> \ 
         <output-ellipsoid-coord-file> <output-spherical-coord-file> \ 
         [output-spec-file]  
         
      Generate inflated, ellipsoid, and spherical coordinate files.
      
      If any of the output coordinate files have an empty name (two 
      consecutive double qutoes "", the coordinate file will not be
      output.  The spec file is optional, and if specified, the generated
      coordinate files will be added to the spec file.  For best results, 
      the fiducial surface must not contain topological defects. 

------------------------------------------------------------------------------
   SURFACE IDENTIFY SULCI
      caret_command -surface-identify-sulci \ 
         <input-spec-file> <input-structure>\ 
         <input-segmentation-volume> <input-closed-topo-file> \
         <input-raw-coord-file> <input-fiducial-coord-file> [write-volume-type]
         
      Create a surface shape file containing depth and curvature measurements,
      a paint file identifying the sulci, and an area color file.  If there 
      is no raw coordinate file, specify fiducial coordinate file instead.

      NOTE: This command MUST be run in the directory containing the files.

      <input-structure> is one of:
         left
         right

      [write-volume-type]   Type of volume files to write.
         Specifies the type of the volume files that will be written
         during the segmentation process.  Valid values are
            AFNI (default)
            NIFTI 
            SPM
            WUNIL

------------------------------------------------------------------------------
   SURFACE INFORMATION
      caret_command -surface-information \ 
         <input-topo-file> <input-coord-file>\ 
         [output-text-file]
         
      Display information about the surface made using the specified
      coordinate and topology files. 

      If the "output-test-file" is not specified, then the information.
      will be printed in the terminal.

------------------------------------------------------------------------------
   SURFACE MAP GYRI WITH DEPTH ROI
      caret_command -surface-map-gyri-with-depth-roi \
         <output-metric-file> <std-mesh-topo-file> \
         <std-mesh-paint-file> <paint-column-number> <paint-name> \
         <std-mesh-fiducial-coord-file-1> <std-mesh-cerebral-hull-coord-file-1>\
         <std-mesh-fiducial-coord-file-2> <std-mesh-cerebral-hull-coord-file-2>\
                       ...                           ...
         <std-mesh-fiducial-coord-file-N> <std-mesh-cerebral-hull-coord-file-N> 
         
      Determine gyral regions associated with sulcal depth ROI.
         
            1) Identify the nodes in the ROI and only process nodes
               that are in the ROI.
            2) For each of the ROI nodes in the hull, find the nearest
               node in the fiducial surface using using Euclidean distance.
            3) Increment the metric value for the nearest fiducial 
               surface node.
            4) Repeat steps 2 thru 3 for each fiducial/hull pair.
         
         Note: Paint column numbers start at 1.


------------------------------------------------------------------------------
   SURFACE SMOOTH AREA
      caret_command -surface-smooth-area \ 
         <f-strength> <i-iterations> <i-edge-iterations> \ 
         <i-project-to-sphere-every-x-iterations> \
         <paint-file-name>  <paint-file-column-name> <paint-name> \
         <input-coord-file-name> <topology-file-name> <output-coord-file-name>
         
      Smooth a region of a surface (coord/topo pair) that is 
      identified by a column in a paint file.  
      Parameters:
         strength  - Percentage of smoothing applied to neighboring
                     nodes.  Ranges from 0 to 1.
         iterations - Number of iterations for which to smooth.
         edge-iterations - smooth edges once every "edge-iterations".
         project-to-sphere-every-x-iterations - Project the surface to
                     a sphere every "this many" iterations.  Set to 
                     zero if the surface is not a sphere.
         paint-file-name - Name of the paint file that contains a 
                     column that identifies the nodes for smoothing.
         paint-file-column-name - Name of the paint file column.
         paint-name - Name in "paint-file-column-name" (eg. MEDIAL.WALL) 
                      that identifies the nodes that are to be smoothed.
         input-coord-file-name - Name of INPUT coordinate file.
         topology-file-name - Name of topology file.
         output-coord-file-name - Name of smoothed OUTPUT coordinate file.
         


------------------------------------------------------------------------------
   SURFACE SPHERICAL REGISTRATION
      caret_command -surface-register-sphere \ 
         <options> <deformation-map-file-containing-registration-parameters> \
         <indiv-spec-file> <atlas-spec-file>   
      
      The above method requires that the each of the spec file have one and only
      one border projection file, closed topology file,fiducial coordinate file,
      and spherical coordinate file.  The spec files may have zero or one
      cut topology file and flat coordinate file. 
      
      
      caret_command -surface-register-sphere \ 
         <options> <deformation-map-file-containing-registration-parameters> \
         <indiv-spec-file> <indiv-border-projection-file>  \ 
         <indiv-closed-topo-file> <indiv-cut-topo-file> \
         <indiv-fiducial-coord-file> <indiv-spherical-coord-file> \
         <indiv-flat-coord-file> \
         <atlas-spec-file> <atlas-border-projection-file>  \ 
         <atlas-closed-topo-file> <atlas-cut-topo-file> \
         <atlas-fiducial-coord-file> <atlas-spherical-coord-file> \
         <atlas-flat-coord-file> 
         
         
      Peform spherical registration.
      
      Some files, such as the flat coordinate files or deformation map file
      are optional and in this case the name should be specified with two
      consecutive double quotes (eg: "").
         
      options - a single character either 'Y' or 'N'   
         Y - deform the individual to the atlas and the atlas to the individual.
         N - deform the individual to the atlas only.
         


------------------------------------------------------------------------------
   SURFACE ROI COORD REPORT
      caret_command -surface-roi-coord-report \ 
         <output-file-name.txt> \
         <input-topo-file-name> \
         <input-paint-file-name> \
         <i-input-paint-file-column> \
         <input-paint-name> \
         <input-coord-file-1> \
         <input-coord-file-2> \
         ...\
         <input-coord-file-N
         
      Print a report listing the mean X, Y, an Z coordinates for 
      the nodes identified by the paint name.  
      
      Note: The paint file column indices start at one.


------------------------------------------------------------------------------
   SURFACE SPHERICAL MULTIRESOLUTION MORPHING
      caret_command -surface-sphere-multi-morph \ 
         <input-spec-file> <input-closed-topo-file>\
         <input-fiducial-coord-file>  <input-spherical-coord-file> \
         
      Peform spherical multi-resolution morphing (distortion correction).


------------------------------------------------------------------------------
   SURFACE SULCAL DEPTH GENERATION
      caret_command -surface-sulcal-depth \ 
         <input-spec-file> <input-closed-topo-file>\
         <input-fiducial-coord-file>  <input-hull-vtk-file> \
         <output-surface-shape-file> <output-hull-coord-file>
         
      Generate sulcal depth.


------------------------------------------------------------------------------
   SURFACE TOPOLOGY DISCONNECT PAINT NODES
      caret_command -surface-topology-disconnect-paint-nodes \ 
         <input-topo-file> <input-paint-file> \
         <input-paint-column-number> <input-paint-name>
         <output-topo-file>
      
      Disconnect all nodes that appear in the specified paint file column
      which use the specified paint name.
      
      Note: Paint file column numbers begin at 1.


------------------------------------------------------------------------------
   SURFACE TOPOLOGY NEIGHBOR LIST
      caret_command -surface-topology-neighbors \ 
         <input-topo-file> <output-text-file> \
         
      For each node in the input topology file, generate a list  
      of the nodes neighbors.  Each line contains the node number   
      which is followed by the node's neighbors.


------------------------------------------------------------------------------
   SURFACE TO CEREBRAL HULL
     caret_command -surface-to-cerebral-hull \ 
     <fiducial-coord-file-name> \
     <closed-topo-file-name> \
     <volume-file-name> \
     <prefix>
     
     Generate a VTK cerebral hull surface for use with -surface-sulcal-depth
     from the fiducial surface, and output to name <prefix>.CerebralHull.vtk.
     NOTE: The volume file must already exist, and will be OVERWRITTEN with
     the segmentation volume of the fiducial surface.  It can be generated
     with -volume-create, and is needed to determine stereotaxic space.


------------------------------------------------------------------------------
   SURFACE CREATE SEGMENTATION
      caret_command -surface-to-segmentation-volume \ 
         <input-coordinate-file> <input-topology-file> \ 
         <output-volume-file> 
         
      Create a segmentation volume from a surface.  The output volume file
      MUST be an existing file that is in the same stereotaxic space as the
      surface.  Run this program with "-volume-create" to create a volume
      file.
      
      Also see "-surface-to-segmentation-volume".

------------------------------------------------------------------------------
   SURFACE TO VOLUME
      caret_command -surface-to-volume \ 
         <input-topo-file> <input-coord-file> \
         <input-metric-paint-or-shape-file> <i-input-column-number> \
         <output-volume-file> \ 
         [f-inner-boundary] [f-outer-boundary] [f-intersection-step]
         
      Intersect a surface with a volume and assign the specified  
      column number's data of the paint, metric, or shape file 
      to the volume.  THE COLUMN NUMBERS START AT ONE.
      
      The volume file must already exist and it must be in the same 
      stereotaxic space as the surface.  A volume file may be created
      by using this program's "-volume-create" command.
      
      The inner boundary, outer boundary, and intersection step parameters
      are optional.  The default values are: 
         inner boundary: -1.5
         outer boundary: 1.5
         intersection step: 0.5


------------------------------------------------------------------------------
   SURFACES TO SEGMENTATION VOLUME MASK
      caret_command -surfaces-to-segmentation-volume-mask \ 
         <input-spec-file> <output-volume-file> \
         [dilation-iterations]
      For each fiducial surface listed in the spec file, convert it
      to a segmentation volume and then merge (union) all of these
      segmentation volumes into a single volume.  Perform the specified
      number of dilation iterations on the output volume prior to 
      saving it.
      
      The output volume must exist and a volume may be created by this
      program using the -volume-create option.
      

------------------------------------------------------------------------------
   VOLUME ANATOMY PEAK ESTIMATION
      caret_command -volume-anatomy-peaks \ 
         <anatomy-volume-name>
         
      Estimate the peaks in an anatomy volume file. 
      

------------------------------------------------------------------------------
   VOLUME BIAS CORRECTION
      caret_command -volume-bias-correction \ 
         <i-gray-minimum> <i-white-maximum> <i-iterations>  \ 
         <input-volume-name> <output-volume-name>
         
      Perform bias correction on a volume. 
      
      "gray-minimum" is a value that is less than but close to the minimum
      value of all gray matter voxels.
      
      "white-maximum" is a value that is greater than but close to the maximum
      value of all white matter voxels.
      
      "iterations" is the number of iterations used in the bias correction
      algorithm.  A value of 5 is sufficient in most cases.
      
      This algorithm was taken from AFNI's 3dUniformize program.

------------------------------------------------------------------------------
   VOLUME BLUR
      caret_command -volume-blur <input-volume-name> <output-volume-name>
         
      Blur the volume. 
      

------------------------------------------------------------------------------
   VOLUME CLASSIFY INTENSITIES
      caret_command -volume-classify-intensity \ 
         <f-mean> <f-low> <f-high> <f-signum> \
         <input-volume-name> <output-volume-name>
         
      Classify intensities.
      

------------------------------------------------------------------------------
   VOLUME COPY VECTOR FILE MAGNITUDE INTO VOXELS
      caret_command -volume-copy-vector-mag \ 
         <vector-file> <input-volume-name> <output-volume-name>
         
      Replace the volume's voxels with the vector file's magnitude.
      

------------------------------------------------------------------------------
   VOLUME CONVERT A VECTOR FILE TO A VOLUME FILE
      caret_command -volume-copy <input-vector-name> <output-volume-name>
         

      Convert a vector file into a vector type volume file,

------------------------------------------------------------------------------
   VOLUME COPY A VOLUME
      caret_command -volume-copy <input-volume-name> <output-volume-name>
         

      Copy a volume.  If the input volume's orientation is valid,
      the output volume will be written in LPI orientation.

------------------------------------------------------------------------------
   VOLUME CREATE
      caret_command -volume-create \
         <i-x-dimension> <i-y-dimension> <i-z-dimension> \
         <output-volume-name>

      caret_command -volume-create \
         <STEREOTAXIC-SPACE> \
         <output-volume-name>

      caret_command -volume-create \
         <i-x-dimension> <i-y-dimension> <i-z-dimension> \
         <f-x-origin> <f-y-origin> <f-z-origin> \
         <f-x-spacing> <f-y-spacing> <f-z-spacing> \
         <ORIENTATION> \ 
         <output-volume-name>

      Create a volume.

      The volume created will have all voxels set to zero.

      The first form in which only the dimensions are specified will have 
      its origin defaulted to zeros, the spacing to ones, and the orienation
      to LPI.

      With the second form, the volume is created in the specified
      stereotaxic space.  Valid spaces are:
            AFNI
            FLIRT
            MACAQUE-F6
            MACAQUE-F99
            MRITOTAL
            SPM
            SPM95
            SPM96
            SPM99
            SPM2
            SPM5
            T88
            711-2B
            711-2B-111
            711-2B-222
            711-2B-333
            711-2C
            711-2C-111
            711-2C-222
            711-2C-333
            711-2O
            711-2O-111
            711-2O-222
            711-2O-333
            711-2Y
            711-2Y-111
            711-2Y-222
            711-2Y-333

      The third form creates a volume using the specified parameters.

      "orientation" consists of three letters from "LRPAIS" where
         L     represents left
         R     represents right
         P     represents posterior
         A     represents anterior
         I     represents inferior
         S     represents superior

------------------------------------------------------------------------------
   VOLUME DILATE
      caret_command -volume-dilate <i-iterations> \
         <input-volume-name> <output-volume-name>
         
      Dilate the volume for the specified number of iterations. 
      

------------------------------------------------------------------------------
   VOLUME DILATE AND ERODE
      caret_command -volume-dilate-erode <i-dialate-iterations> \
         <i-erode-iterations> \
         <input-volume-name> <output-volume-name>
         
      Dilate and erode the volume for the specified number of iterations. 
      

------------------------------------------------------------------------------
   VOLUME DILATE AND ERODE WITHIN MASK
      caret_command -volume-dilate-erode-mask \
         <i-dialate-iterations> <i-erode-iterations> \
         <i-min-x> <i-max-x> <i-min-y> <i-max-y> <i-min-z> <i-max-z> \
         <input-volume-name> <output-volume-name>
         
      Dilate and erode the volume for the specified number of iterations.
      Only voxels within extent are modified.
      

------------------------------------------------------------------------------
   VOLUME ERODE
      caret_command -volume-erode <i-iterations> \
       <input-volume-name> <output-volume-name>
         
      Erode the volume for the specified number of iterations. 
      

------------------------------------------------------------------------------
   VOLUME EULER COUNT
      caret_command -volume-euler \
          <i-min-x> <i-max-x> <i-min-y> <i-max-y> <i-min-z> <i-max-z> \
          <input-volume-name>
         
      Perform and print the Euler Counts for a segmentation volume. 
      

------------------------------------------------------------------------------
   VOLUME FILL BIGGEST OBJECT
      caret_command -volume-fill-biggest-object  \
         <i-min-x> <i-max-x> <i-min-y> <i-max-y> <i-min-z> <i-max-z> \
         <input-volume-name> <output-volume-name>
         
      Fill the biggest object with extent and remove all islands.
      

------------------------------------------------------------------------------
   VOLUME FILL HOLES
      caret_command -volume-fill-holes \ 
         <input-volume-name> <output-volume-name>
         
      Fill holes (cavities) in a segmentation volume.
      

------------------------------------------------------------------------------
   VOLUME FILL SLICE
      caret_command -volume-fill-slice \ 
         <axis> <i-seed-x> <i-seed-y> <i-seed-z>
         <input-volume-name> <output-volume-name>
         
      Flood fill a single slice.
      

------------------------------------------------------------------------------
   VOLUME FIND LIMITS
      caret_command -volume-find-limits <input-volume-name> <limits-file-name>
         
      Find the limits (non-zero voxel extent) of the volume.
      

------------------------------------------------------------------------------
   VOLUME FLOOD FILL
      caret_command -volume-flood-fill \ 
         <i-seed-x> <i-seed-y> <i-seed-z> \
         <input-volume-name> <output-volume-name>
         
      Flood fill the object starting at seed x/y/z.  All 
      voxels not connected to seed are set to zero.
      

------------------------------------------------------------------------------
   VOLUME GRADIENT
      caret_command -volume-gradient \ 
         <i-lambda> <b-grad-flag> <b-mask-flag>  \
         <input-volume-name> <mask-volume-name> <gradient-vector-file-name>
         
      Compute a gradient.
      

------------------------------------------------------------------------------
   VOLUME HISTOGRAM
      caret_command -volume-histogram \ 
         <volume-file-name> [b-list-peaks] [i-number-of-buckets] [i-Y-Maximum]
         
      Display a histogram of the volume in the terminal window.
      
      If "list-peaks" is true, the numerical estimates of the 
      gray and white matter peaks will be listed.
      
      if "number-of-buckets" is not specified, the histogram will
      contain 64 buckets.
      
      If "Y-Maximum" is not specified, the maximum Y-value will be
      500000.
      

------------------------------------------------------------------------------
   VOLUME INFORMATION
      caret_command -volume-info <volume-file-name>
         
      Print information about the volume file.
      

------------------------------------------------------------------------------
   VOLUME INTERSECT VOLUME WITH SURFACE
      caret_command -volume-intersect-volume-with-surface \ 
         <paint-name>  X  Y  Z  <input-volume> <spec-file>
         
      Intersect a volume with a surface and for all nodes that
      intersect a non-zero voxel, assign "paint-name" to that node.
      A paint file named "<paint-name>.paint" is created. 
      The surface is offset by the X, Y, Z values.
      

------------------------------------------------------------------------------
   VOLUME MAKE PLANE
      caret_command -volume-make-plane \ 
         <x-slope> <x-offset> <y-slope> <y-offset> <z-slope> <z-offset> \
         <offset> <thickness> <input-volume-name> <output-volume-name>
         
      Make plane.
      

------------------------------------------------------------------------------
   VOLUME MAKE RECTANGLE
      caret_command -volume-make-rectangle \ 
         <i-min> <i-max> <j-min> <j-max> <k-min> <k-max> <f-voxel-value>\
         <input-volume-name> <output-volume-name>
         
      Set the voxels within the range [i-min, i-max), .
      [j-min, j-max), [k-min, k-max) to the specified value.
      

------------------------------------------------------------------------------
   VOLUME MAKE SHELL
      caret_command -volume-make-shell \ 
         <i-num-dilation> <i-num-erosion> \
         <input-volume-name> <output-volume-name>
         
      Make shell.
      

------------------------------------------------------------------------------
   VOLUME MAKE SPHERE
      caret_command -volume-make-sphere \ 
         <i-center-x> <i-center-y> <i-center-z> <f-radius> \
         <input-volume-name> <output-volume-name>
         
      Make a sphere within the volume.
      

------------------------------------------------------------------------------
   VOLUME MATHEMATICAL OPERATIONS ON VOLUMES
      caret_command -volume-math <operation> \ 
         <input-volume-1-name> <input-volume-2-name> \
         <input-volume-3-name> <output-volume-name>
         
      If <input-volume-3-name> is only required for the operation
      "DIFF_RATIO".  For all other operations, specify its name as "NULL".

      Perform mathematical operations on volumes.
         "operation" is one of: 
            ADD
            AND
            DIFF_RATIO
            DIVIDE
            MAX
            MULTIPLY
            NAND
            NOR
            OR
            PAINT_COMBINE
            SQRT
            SUBTRACT
            SUBTRACT_POSITIVE  (subtract and if result < 0, result = 0)
      

------------------------------------------------------------------------------
   VOLUME MATHEMATICAL OPERATIONS (UNARY) ON A VOLUME
      caret_command -volume-math-unary <operation> <f-scalar> \ 
         <input-volume-name> <output-volume-name>
         
      Perform mathematical operations on a volume.
         "operation" is one of: 
            ADD_SCALAR
            ABS_VALUE
            CEILING
            FIX_NOT_A_NUMBER
            FLOOR
            MULTIPLY_SCALAR
      

------------------------------------------------------------------------------
   VOLUME MASK VOLUME
      caret_command -volume-mask-volume \ 
         <i-min-x> <i-max-x> <i-min-y> <i-max-y> <i-min-z> <i-max-z> \
         <input-volume-name> <output-volume-name>
         
      Clear all of the voxels outside the specified extent. 
      
      caret_command -volume-mask-volume <i-dilation-iterations>\ 
         <input-volume-name> <mask-volume> <output-volume-name>
         
      Clear all of the voxels in the input volume that do map into 
      a non-zero voxel in the mask volume.  The mapping is performed
      using stereotaxic coordinates so the volumes do not need to have
      have the same dimensions but must overlap in stereotaxic 
      coordinates.  Create a mask volume using this program with the
      "-volume-segment-mask-creation" option.
      
      If "dilation-iterations" is non-zero, the mask will be dilated
      the specified number of times prior to the application of the mask.
      

------------------------------------------------------------------------------
   VOLUME NEAR TO PLANE
      caret_command -volume-near-to-plane \ 
         <f-sigma-N> <f-sigma-W> <f-offset> <b-down-flag> <i-grad-sign> \
         <b-masking-flag> <vector-file-name> \
         <mask-volume-name> <output-volume-name>
         
      Near to plane.
      

------------------------------------------------------------------------------
   VOLUME PAD A VOLUME
      caret_command -volume-pad-volume <i-pad-neg-x> <i-pad-pos-x> <i-pad-neg-y> \
      <i-pad-pos-y> <i-pad-neg-z> <i-pad-pos-z> \
      <input-volume-name> <output-volume-name>
         
      Add padding around a volume.
      

------------------------------------------------------------------------------
   VOLUME REMOVE ISLANDS
      caret_command -volume-remove-islands <input-volume-name> \
       <output-volume-name>
         
      Remove islands from a segmentation volume.
      

------------------------------------------------------------------------------
   VOLUME RESAMPLE
      caret_command -volume-resample \ 
         <f-new-spacing-x> <f-new-spacing-y> <f-new-spacing-z> \
         <input-volume-name> <output-volume-name>
         
      Resample the volume to the specified spacing.
      

------------------------------------------------------------------------------
   VOLUME RESIZE
      caret_command -volume-resize \ 
         <i-x-min> <i-x-max> <i-y-min> <i-y-max> <i-z-min> <i-z-max> \
         <input-volume-name> <output-volume-name>
         
      Resize the volume.  If "min" values are less than zero,
      voxels will be added to that side of the volume.

------------------------------------------------------------------------------
   VOLUME RESCALE VOXELS
      caret_command -volume-rescale \ 
         <f-input-min> <f-input-max> <f-output-min> <f-output-max> \ 
         <input-volume-name> <output-volume-name> 
         
      Rescale a volume's voxels.
      "input-min" and below are mapped to "output-min".
      "input-max" and above are mapped to "output-max".
      

------------------------------------------------------------------------------
   VOLUME SCALE VOXELS 0 to 255 WITH PERCENTAGE OF MIN/MAX
      caret_command -volume-scale-percent-min-max-255 \ 
         <percent-minimum> <percent-maximum> \
         <input-volume-name> <output-volume-name>
         
      Scale voxels so that they are in the range 0 to 255 but 
      map the first "percent-minimum" voxels to 0 and map the
      last "percent-maximum" voxels to 255.
      
      The "percent-minimum" and "percent-maximum" values should
      range from 0.0 to 100.0.  Setting the "percent-minimum" to 
      2.0 and the "percent-maximum" to 3.0 will result in the first
      two percent of voxel values being mapped to zero and the last
      three percent of voxel values being mapped to two hundred 
      fifty five.

------------------------------------------------------------------------------
   VOLUME SCALE VOXELS 0 to 255
      caret_command -volume-scale-255 \ 
         <input-volume-name> <output-volume-name>
         
      Scale voxels so that they are in the range 0 to 255.
      

------------------------------------------------------------------------------
   VOLUME SCULPT
      caret_command -volume-sculpt \ 
         <i-min-x> <i-max-x> <i-min-y> <i-max-y> <i-min-z> <i-max-z> \
         <i-seed-x> <i-seed-y> <i-seed-z> \
         <mode> <i-num-steps> <other-volume> \ 
         <input-volume-name> <output-volume-name>

      Sculpt a volume.
      "mode" is one of:
          AND
          SEED-AND
          AND-NOT
          SEED-AND-NOT
      

------------------------------------------------------------------------------
   VOLUME SEGMENTATION
      caret_command -volume-segment <operation_code> \
                <f-gray-peak> <f-white-peak> \
                <padding-code> <structure> <spec-file-name> 
                <anat-or-segment-volume> [write-volume-type]

      Operation_Code characters
         Specify each with either a "Y" or "N".
         All characters must be specified.
         Character   Operation Description
         ---------   ---------------------
                 1   Disconnect Eye and Skull
                 2   Disconnect Hindbrain
                 3   Use High Threshold for Hindbrain disconnection
                 4   Cut Corpus Callossum
                 5   Generate Segmentation
                 6   Fill Ventricles
                 7   Automatic Error Correction
                 8   Generate Raw and Fiducial Surfaces
                 9   Reduce polygons in surfaces
                10   Correct topological errors in surfaces
                11   Generate Inflated Surface
                12   Generate Very Inflated Surface
                13   Generate Ellipsoid Surface (For Flattening)
                14   Generate Hull Surface 
                15   Generate Curvature, Depth, and Paint Attributes

      gray-peak  specifies the intensity of the gray matter peak in the 
                 anatomy volume.

      white-peak  specifies the intensity of the white matter peak in the
                  anatomy volume.

      padding-code
         Specify padding for any cut faces when segmenting a partial hemisphere.
         Specify each with either a "Y" for padding or "N" for no padding.
         All characters must be specified.
         Character   Padding Description
         ---------   -------------------
                 1   Pad Negative X
                 2   Pad Positive X
                 3   Pad Posterior Y
                 4   Pad Anterior Y
                 5   Pad Inferior Z
                 6   Pad Superior Z

      structure  Specifies the brain structure.
                  Acceptable values are RIGHT or LEFT

      spec-file-name  Name of specification file.

      anat-or-segment-volume  Name of input volume.
         The volume must be in a Left-Posterior-Inferior orientation and
         its stereotaxic coordinates must be set so that the origin is 
         at the anterior commissure.

      write-volume-type   Type of volume files to write.
         Specifies the type of the volume files that will be written
         during the segmentation process.  Valid values are
            AFNI
            NIFTI (default)
            SPM
            WUNIL

------------------------------------------------------------------------------
   VOLUME SEGMENTATION STEREOTAXIC SPACE
      caret_command -volume-segment-stereo-space \
         [-ecv] \
         [-ecs] \
         [-flat] \
         [-mp] \
         [-noeye] \
         <spec-file-name> \
         <anatomical-volume-file-name> 

      THIS IS EXPERIMENTAL BUT IT WILL PRODUCE A SURFACE

      The input spec file must contain the stereotaxic space and the 
      structure (LEFT or RIGHT) for this command to operate.  A spec
      is created by running this program with the "-spec-file-create"
      command.

      This input volume must be in one of the supported stereotaxic
      spaces with the origin at the anterior commissure.  The volume
      should not have non-uniformity (bias) problems.  The input
      volume is cropped to a single hemisphere, the voxels are
      mapped to the range 0 to 255, the gray and white matter
      histogram peaks are estimated, the volume is segmented, and
      fiducial and inflated surfaces are generated.

      Stereotaxic Spaces Supported
         711-2C      LEFT
         711-2C      RIGHT
         AFNI        LEFT
         AFNI        RIGHT
         CCHMC       LEFT
         CCHMC       RIGHT
         FLIRT       LEFT
         FLIRT       RIGHT
         MRITOTAL    LEFT
         MRITOTAL    RIGHT
         SPM2        LEFT
         SPM2        RIGHT
         SPM99       LEFT
         SPM99       RIGHT
      
      OPTIONS
         -ecv   Perform error correction of the segmentation volume.
      
         -ecs   Perform error correction of the surface.
      
         -flat  Generate files for flattening (very inflated, ellipsoidal,
                paint, and surface shape.
      
         -mp    Generate surface with maxmimum number of polygons.
      
         -noeye  Do NOT disconnect eye and strip skull
      
      

------------------------------------------------------------------------------
   VOLUME SEGMENTATION MASK CREATION
      caret_command -volume-segment-mask-creation <i-dilation-iterations> \
                <output-volume-name> <one-or-more-input-segmentation-volumes> 

         Create a segmentation mask volume by merging a group of 
         segmentation volumes.  The merging is done using stereotaxic
         coordinates so the input volumes may be different dimensions.
         The output volume will have the same dimensions and 
         stereotaxic coordinates as the first input volume file.
         If you want the output volume to have specific dimensions
         or coordinates, use this program with the option
         "-volume-create" to create an empty input volume and
         specify this empty volume as the first input volume file.

         Dilation is optional so use a value of zero if you do not
         want the mask dilated after merging all of the input volume
         files.

         Apply a mask using this program with the "-volume-mask-volume"
         option.

------------------------------------------------------------------------------
   VOLUME SET ORIENTATION
      caret_command -volume-set-orientation \ 
         <orientation> <input-volume-name> <output-volume-name> 
         
      Set the orientation for the volume file.
      "orientation" consists of three letters from "LRPAIS" where
         L     represents left
         R     represents right
         P     represents posterior
         A     represents anterior
         I     represents inferior
         S     represents superior
      

------------------------------------------------------------------------------
   VOLUME SET ORIGIN
      caret_command -volume-set-origin \ 
         <f-origin-x> <f-origin-y> <f-origin-z> \
         <input-volume-name> <output-volume-name>
         
      Set the origin for the volume file.
      

------------------------------------------------------------------------------
   VOLUME SET SPACING
      caret_command -volume-set-spacing \ 
         <f-spacing-x> <f-spacing-y> <f-spacing-z> \
         <input-volume-name> <output-volume-name>
               Set the voxel spacing for the volume file.
      

------------------------------------------------------------------------------
   VOLUME SHIFT AXIS
      caret_command -volume-shift-axis \ 
         <axis> <i-offset> \
         <input-volume-name> <output-volume-name>
         
      Shift along an axis.
      "axis" is one of "X", "Y", or "Z".
      

------------------------------------------------------------------------------
   VOLUME SMEAR AXIS
      caret_command -volume-smear-axis \ 
         <axis> <i-mag> <i-sign> <i-core> \
         <input-volume-name> <output-volume-name>
         
      Smear along an axis.
      "axis" is one of "X", "Y", or "Z".
      

------------------------------------------------------------------------------
   VOLUME THRESHOLDING
      caret_command -volume-threshold <f-value> \
         <input-volume-name> <output-volume-name>
         
      Voxels less than "value" are set to zero.  Voxels greater than 
      or equal to "value" are set to 255.
      

------------------------------------------------------------------------------
   VOLUME THRESHOLDING DUAL
      caret_command -volume-threshold-dual <f-value-low> <f-value-high>  \
         <input-volume-name> <output-volume-name>
         
      Voxels between <value-low>  and <value-high> are set to 255.
      All other voxels are set to 0.
      

------------------------------------------------------------------------------
   VOLUME THRESHOLDING INVERSE
      caret_command -volume-threshold-inverse <f-value> \
         <input-volume-name> <output-volume-name>
         
      Voxels greater than "value" are set to zero.  Voxels less than 
      or equal to "value" are set to 255.
      

------------------------------------------------------------------------------
   VOLUME VECTOR FILES COMBINE
      caret_command -volume-vector-combine \ 
         <operation> <b-mask-flag> <mask-volume-name>   \
         <input-vector-1-name> <input-vector-2-name> <output-vector-name>
         
      Combine vector files.
         "operation" is one of:
            DOT_SQRT_RECT_MINUS
            2_VEC_NORMAL
            2_VEC

------------------------------------------------------------------------------
   VOLUME VECTOR MAGNITUDE - REPLACE WITH VOLUME
      caret_command -volume-vector-replace-mag-volume \ 
         <operation> <volume-file>    \
         <input-vector-name> <output-vector-name>
         
      Replace vector file's magnitude.
         "operation" is one of:
            REPLACE  - replace magnitude with volume's voxel
            MULTIPLY - multiply magnitude with volume's voxel