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

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 hyperbolic 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 hyperbolic tangent of the argument sinc: 1 argument, sinc(0) = 1, sin(x) / x otherwise 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)