vcylarim_getmask

The program vcylarim_getmask can be used to obtain an initial brain mask. The idea is to exclude brain regions where values in the activation map are too small to be relevant for laminar-specific analysis.

Just like the main tool vcylarim the program begins by generating cylinders. It then computes the largest and the smallest value of the activation map within each cylinder. In voxels where cylinders overlap, the obtained min/max z-values are averaged.

The program outputs a map of min/max z-values. This map can then be thresholded to obtain a mask to be used in subsequent calls to vcylarim.

Example:

vcylarim_getmask -in zmap.v -out cylmask.v -rim rim.v -metric metric.v -radius 3

Parameters of ‘vcylarim_getmask’

-help

Prints usage information.

-in

Input file.

-out

Output file.

-mask

Region of interest mask (Optional)

-metric

Metric image (required)

-rim

Rim image (required)

-radius

Cylinder radius in mm. Default: 2

-j

Number of processors to use, ‘0’ to use all. Default: 0