Using Workbench Command

UPDATE SCENE FILE
   wb_command -scene-file-update
      <input-scene-file> - the input scene file
      <output-scene-file> - the new scene file to create
      <scene-name-or-number> - name or number (starting at one) of the scene in
         the scene file

      [-fix-map-palette-settings] - Fix palette settings for files with change
         in number of maps

      [-remove-missing-files] - Remove missing files from SpecFile

      [-error] - Abort command if there is an error performing any of the
         operations on the scene file

      [-verbose] - Print names of files that have palettes updated

      [-copy-map-one-palette] - repeatable - Copy palettes settings from first
         map to all maps in a data file
         <Data File Name Suffix> - Name of palette mapped data file (cifti,
            metric, volume)

      [-data-file-add] - repeatable - Add a data file to scene's loaded files
         <Name of data file> - Name of data file.  If a data file not in the
            current directory, it is best to use an absolute path (a relative
            path may work).  Instead of a data file, this value may be the name
            of a text file (must end in ".txt") that contains the names of one
            or more data files, one per line.
         Example on UNIX to create a text file containing all CIFTI scalar
            files in the current directory with absolute paths:
            ls -d $PWD/*dscalar.nii  > file.txt

      [-data-file-remove] - repeatable - Remove a data file from scene's loaded
         files
         <Name of data file> - Name of data file.  If a data file not in the
            current directory, it is best to use an absolute path (a relative
            path may work).  Instead of a data file, this value may be the name
            of a text file (must end in ".txt") that contains the names of one
            or more data files, one per line.
         Example on UNIX to create a text file containing all CIFTI scalar
            files in the current directory with absolute paths:
            ls -d $PWD/*dscalar.nii  > file.txt

      This command will update a scene for specific changes in data files.

      "-fix-map-palette-settings" will find all data files that have had a
      change in the number of maps since the scene scene was created.  If the
      file has its "Apply to All Maps" property enabled, the palette setting in
      the first map is copied to all maps in the file.  Note: This modifies the
      palette settings for the file in the scene (data file is NOT modified).

      "-copy-map-one-palette" will copy the palette settings from the first map
      to all other maps in a data file.  This option is typically used when the
      number of maps in a data file changes.  It changes the palette settings
      in the scene that are applied to the data file when the scene is loaded
      (the data file is not modified).  The name of the data file specified on
      the command line is matched to the end of file names in the scene.  This
      allows matching multiple files if their names end with the same
      characters.  It also allows including a relative path when there is more
      than one file with the same name but in different paths and only one of
      the files to be updated.

      "-remove-missing-files" Any files that fail to load when the scene is
      read will be removed from the scene.  Thus, if one deletes files prior to
      running with this option, the deleted files are removed from the scene.  

      "-error" If this option is provided and there is an error while
      performing any of the scene operations, the command will immediately
      cease processing and the output scene file will not be created.
      Otherwise any errors will be listed after the command finishes.