overlay_mask

• purpose
• usage
• examples
• comments
• error messages
• see also

Purpose:

Voxels corresponding to a mask are set to maximum intensity before saving

Usage:

overlay_mask mask base output [options]

options:

[-o]

grants permission to overwrite output

[-t threshold]

overlays only voxels from mask that are greater than or equal to threshold

where the following definitions apply:

mask

the name of the mask file

base

the name of the file that is modified based on the mask

output

the name of the output file created

threshold

only mask values greater than or equal to this value are used

Examples:

• all voxels with intensities greater than or equal to 16384 in the file 'activations' are set to maximum intensity in the spatially equivalent file 'mri' and the result is saved as 'paintedmri'.

Comments:

• the mask file can be a 1-bit 'binary' file, in which case no threshold should be specified
• The value of threshold should be specified with respect to the actual values in the input file. You should not attempt to compensate for how AIR will map these values to their internal representation or to the output file values. This program will automatically map the values that you specify to the corresponding internal values.

Error messages: (alphabetical by case)

A threshold value must follow -t

• supply an integer value

Sorry, flag -____ is not defined for this program

• check syntax for undefined flags

unable to parse arguments, expected argument ____ to start with a '-'

• check syntax, an argument without a flag is positioned as if were a flag

See also:

• binarize
• binarymask