Using Workbench Command

Workbench Command is a set of command-line tools that can be used to perform simple and complex operations within Connectome Workbench.

Full Documentation:

Documentation Home
EVALUATE EXPRESSION ON VOLUME FILES
   wb_command -volume-math
      <expression> - the expression to evaluate, in quotes
      <volume-out> - output - the output volume

      [-fixnan] - replace NaN results with a value
         <replace> - value to replace NaN with

      [-var] - repeatable - a volume file to use as a variable
         <name> - the name of the variable, as used in the expression
         <volume> - the volume file to use as this variable

         [-subvolume] - select a single subvolume
            <subvol> - the subvolume number or name

         [-repeat] - reuse a single subvolume for each subvolume of calculation

      This command evaluates <expression> at each voxel independently.  There
      must be at least one -var option (to get the volume space from), even if
      the <name> specified in it isn't used in <expression>.  All volumes must
      have the same volume space.  Filenames are not valid in <expression>, use
      a variable name and a -var option with matching <name> to specify an
      input file.  If the -subvolume option is given to any -var option, only
      one subvolume is used from that file.  If -repeat is specified, the file
      must either have only one subvolume, or have the -subvolume option
      specified.  All files that don't use -repeat must have the same number of
      subvolumes requested to be used.  The format of <expression> is as
      follows:

      Expressions consist of constants, variables, operators, parentheses, and
      functions, in infix notation, such as 'exp(-x + 3) * scale'.  Variables
      are strings of any length, using the characters a-z, A-Z, 0-9, and _, but
      may not take the name of a named constant.  Currently, there is only one
      named constant, PI.  The operators are +, -, *, /, ^, >, <, >=, <=, ==,
      !=, !, &&, ||.  These behave as in C, except that ^ is exponentiation,
      i.e. pow(x, y), and takes higher precedence than other binary operators
      (also, '-3^-4^-5' means '-(3^(-(4^-5)))').  The <=, >=, ==, and !=
      operators are given a small amount of wiggle room, equal to one millionth
      of the smaller of the absolute values of the values being compared.

      Comparison and logical operators return 0 or 1, you can do masking with
      expressions like 'x * (mask > 0)'.  For all logical operators, an input
      is considered true iff it is greater than 0.  The expression '0 < x < 5'
      is not syntactically wrong, but it will NOT do what is desired, because
      it is evaluated left to right, i.e. '((0 < x) < 5)', which will always
      return 1, as both possible results of a comparison are less than 5.  A
      warning is generated if an expression of this type is detected.  Use
      something like 'x > 0 && x < 5' to get the desired behavior.

      Whitespace between elements is ignored, ' sin ( 2 * x ) ' is equivalent
      to 'sin(2*x)', but 's in(2*x)' is an error.  Implied multiplication is
      not allowed, the expression '2x' will be parsed as a variable.
      Parentheses are (), do not use [] or {}.  Functions require parentheses,
      the expression 'sin x' is an error.

      The following functions are supported:

         sin: 1 argument, the sine of the argument (units are radians)
         cos: 1 argument, the cosine of the argument (units are radians)
         tan: 1 argument, the tangent of the argument (units are radians)
         asin: 1 argument, the inverse of sine of the argument, in radians
         acos: 1 argument, the inverse of cosine of the argument, in radians
         atan: 1 argument, the inverse of tangent of the argument, in radians
         atan2: 2 arguments, atan2(y, x) returns the inverse of tangent of
      (y/x), in radians, determining quadrant by the sign of both arguments
         sinh: 1 argument, the hyperbolic sine of the argument
         cosh: 1 argument, the hyperbolic cosine of the argument
         tanh: 1 argument, the hyperboloc tangent of the argument
         asinh: 1 argument, the inverse hyperbolic sine of the argument
         acosh: 1 argument, the inverse hyperbolic cosine of the argument
         atanh: 1 argument, the inverse hyperboloc tangent of the argument
         ln: 1 argument, the natural logarithm of the argument
         exp: 1 argument, the constant e raised to the power of the argument
         log: 1 argument, the base 10 logarithm of the argument
         log2: 1 argument, the base 2 logarithm of the argument
         sqrt: 1 argument, the square root of the argument
         abs: 1 argument, the absolute value of the argument
         floor: 1 argument, the largest integer not greater than the argument
         round: 1 argument, the nearest integer, with ties rounded away from
      zero
         ceil: 1 argument, the smallest integer not less than the argument
         min: 2 arguments, min(x, y) returns y if (x > y), x otherwise
         max: 2 arguments, max(x, y) returns y if (x < y), x otherwise
         mod: 2 arguments, mod(x, y) = x - y * floor(x / y), or 0 if y == 0
         clamp: 3 arguments, clamp(x, low, high) = min(max(x, low), high)