mincbbox

calculate the bounding box of non-zero data in a MINC volume

mincbbox [<options>] <inputfile>

DESCRIPTION

mincbbox calculates the bounding box of the data in a MINC volume and returns the coordinates of the box in terms of start position and width in millimetres along each spatial axis.

The program iterates over all voxels in the input volume and finds the minimum and maximum world coordinates of voxels whose value exceeds a configurable threshold (default 0). The output can be formatted for direct use with other MINC tools such as mincresample or mincreshape.

OPTIONS

-threshold value

Set the real-value threshold for determining the bounding box. Voxels with values greater than this threshold are considered to be inside the bounding box. Default: 0.

-one_line

Output on one line (default): start_x start_y start_z width_x width_y width_z.

-two_lines

Output on two lines: start coordinates on the first line, widths on the second.

-mincresample

Output in a format suitable for passing directly to mincresample: -step x y z -start x y z -nelements x y z.

-mincreshape

Output in a format suitable for passing directly to mincreshape: -start x,y,z -count dx,dy,dz.

-minccrop

Output in a format suitable for autocropping: -xlim x1 x2 -ylim y1 y2 -zlim z1 z2.

-verbose

Write messages indicating progress (default).

-quiet

Do not write log messages.

-debug

Print out debugging information.

-help

Print summary of command-line options and exit.

-version

Print the program’s version number and exit.

EXAMPLES

Print the bounding box of a volume:

mincbbox input.mnc

Print the bounding box using a threshold of 10:

mincbbox -threshold 10 input.mnc

Resample a volume to its bounding box:

mincresample input.mnc output.mnc $(mincbbox -mincresample input.mnc)

AUTHOR

Louis Collins - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.

COPYRIGHTS

Copyright © 1994 by Louis Collins

SEE ALSO

mincresample mincreshape autocrop