Workbench Command is a set of command-line tools that can be used to perform simple and complex operations within Connectome Workbench.
SMOOTH A METRIC FILE wb_command -metric-smoothing <surface> - the surface to smooth on <metric-in> - the metric to smooth <smoothing-kernel> - the sigma for the gaussian kernel function, in mm <metric-out> - output - the output metric [-roi] - select a region of interest to smooth <roi-metric> - the roi to smooth within, as a metric [-match-columns] - for each input column, use the corresponding column from the roi [-fix-zeros] - treat zero values as not being data [-column] - select a single column to smooth <column> - the column number or name [-corrected-areas] - vertex areas to use instead of computing them from the surface <area-metric> - the corrected vertex areas, as a metric [-method] - select smoothing method, default GEO_GAUSS_AREA <method> - the name of the smoothing method Smooth a metric file on a surface. By default, smooths all input columns on the entire surface, specify -column to use only one input column, and -roi to smooth only where the roi metric is greater than 0, outputting zeros elsewhere. When using -roi, input data outside the ROI is not used to compute the smoothed values. By default, the first column of the roi metric is used for all input columns. When -match-columns is specified to the -roi option, the input and roi metrics must have the same number of columns, and for each input column's index, the same column index is used in the roi metric. If the -match-columns option to -roi is used while the -column option is also used, the number of columns must match between the roi and input metric, and it will use the roi column with the index of the selected input column. The -fix-zeros option causes the smoothing to not use an input value if it is zero, but still write a smoothed value to the vertex. This is useful for zeros that indicate lack of information, preventing them from pulling down the intensity of nearby vertices, while giving the zero an extrapolated value. The -corrected-areas option is intended for when it is unavoidable to smooth on a group average surface, it is only an approximate correction for the reduction of structure in a group average surface. It is better to smooth the data on individuals before averaging, when feasible. Valid values for <method> are: GEO_GAUSS_AREA - uses a geodesic gaussian kernel, and normalizes based on vertex area in order to work more reliably on irregular surfaces GEO_GAUSS_EQUAL - uses a geodesic gaussian kernel, and normalizes assuming each vertex has equal importance GEO_GAUSS - matches geodesic gaussian smoothing from caret5, but does not check kernels for having unequal importance The GEO_GAUSS_AREA method is the default because it is usually the correct choice. GEO_GAUSS_EQUAL may be the correct choice when the sum of vertex values is more meaningful then the surface integral (sum of values .* areas), for instance when smoothing vertex areas (the sum is the total surface area, while the surface integral is the sum of squares of the vertex areas). The GEO_GAUSS method is not recommended, it exists mainly to replicate methods of studies done with caret5's geodesic smoothing.