vbstatmap

From VoxBoWiki

vbstatmap is a command-line tool that makes it easy to create statistical maps from a VoxBo GLM directory.

To produce a given statistical map, vbstatmap needs to know the following:

1. the path of the glm directory
2. a filename for the stat cube to be produced
3. the desired contrast

Optionally, for t-maps the user may use variance smoothing. Note that the resulting statistical values are not really t-values, and cannot be tested against the t-distribution. They are generally used with a Permutation test.

The best way to specify the desired contrast is using a Contrast file, because that way you can refer to a contrast by name (and contrary to the help text, it doesn't need to be in quotes unless it has spaces in it). You can also specify a contrast vector (weights for each of the covariates of interest) on the command line, but we don't recommend it.

Here's the help text:

VoxBo vbstatmap (v1.8.5pre4/Aug 22 2008)
summary: creates a stat map from a GLM directory
usage:
    vbstatmap <glm dir> [flags]
flags:
    -s <scale>        scale, default creates a t-map
    -q <num>          q value for an FDR test
    -c <contrast>     contrast name or vector
    -o <file>         output file
    -p <x> <y> <z>    FWHM in voxels for pseudo-t variance smoothing
    -m <path/file>    relative path and file name to mask cube.
example:
    vbstatmap myglm_directory -o out.cub -c "1 0" -s 0 0 0
scales:
    t                  - t value map
    i                  - intercept term percent change map
    beta or rb         - raw beta values map
    f                  - F value map
    tp tp/1 tp/2       - p map of t values
    fp                 - p map for F values
    tz tz/1 tz/2       - Z map of t values
    fz                 - Z map for F values
notes:
    if you use -c to specify a conrast vector, include only covariates
      of interest, and enclose the vector in quotes, e.g.: -c "1 0 -1"
    use the -p option to smooth the variance map for a pseudo-t map
    note that VoxBo defaults to one tailed tests, and that
      /1 and /2 force one tailed and two tailed for p and z maps