vbstatmap

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 (v1.8.5/Jun 14 2011)
summary: creates a stat map from a GLM directory
usage:
    vbstatmap <glm dir> [flags]
flags:
    -c <contrast>     contrast name or vector
    -o <file>         output file
    -p <x> <y> <z>    FWHM in voxels for pseudo-t variance smoothing
    -m <mask>         mask volume
    -q <num>          q value for an FDR test
example:
  vbstatmap myglm_directory -o out.cub -c "foo t vec 1 0" -p 0 0 0
notes:

  You are strongly encouraged to specify your contrasts in the
  contrasts.txt file, which is automatically created along with your
  GLM, and comes with comments explaining its use.  Then you can just
  use the -c flag with the name of a contrast in that file (e.g., "-c
  mycontrast").  If you want to specify the contrast on the command
  line, it's best to use that same syntax, e.g.: -c "foo t vec 1 0
  -1".  Note that the first token ("foo") isn't used for anything
  right now.  For more information on specifying contrasts, type
  "vbtool contrast"

  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

  If you provide a q value of 0 (-q 0), vbstatmap will give you FDR
  thresholds for a range of commonly requested q values.