make_phantom

create a synthetic MINC volume containing a geometric phantom object

make_phantom [<options>] output.mnc

DESCRIPTION

make_phantom creates a synthetic MINC volume containing a geometric phantom, either a rectangle or an ellipsoid. The user specifies volume parameters (number of elements, step sizes, start coordinates, data type) and object parameters (center, width, fill value, edge value, background value).

For rectangular phantoms, all voxels whose world coordinates fall within the specified bounding box are set to the fill value. For ellipsoidal phantoms, the standard ellipsoid equation is used to determine membership, with optional partial-volume effects computed via sub-voxel sampling.

This tool is primarily used for generating synthetic test data for registration and other image processing algorithms.

OPTIONS

Object definition options

-rectangle: Build a rectangular object (default).
-ellipse: Build an ellipsoidal object.
-center x y z: Center point of the object in world coordinates. Default: 128 128 128.
-xcenter value: Center of the object in the X dimension. Default: 128.
-ycenter value: Center of the object in the Y dimension. Default: 128.
-zcenter value: Center of the object in the Z dimension. Default: 128.
-width wx wy wz: Width of the object in world millimetres along X, Y, and Z. Default: 60 80 30.
-xwidth value: Width of the object in the X dimension. Default: 60.
-ywidth value: Width of the object in the Y dimension. Default: 80.
-zwidth value: Width of the object in the Z dimension. Default: 30.
-fill_value value: Real value used to fill the interior of the object. Default: 1.
-edge_value value: Real value used for edge voxels of the object. Default: 1.
-background value: Real value used for background voxels. Default: 0.
-no_partial: Do not account for partial volume effects at object boundaries.

Volume definition options

-nelements nx ny nz: Number of elements (voxels) along each dimension. Default: 128 128 128.
-xnelements value: Number of elements along the X dimension. Default: 128.
-ynelements value: Number of elements along the Y dimension. Default: 128.
-znelements value: Number of elements along the Z dimension. Default: 128.
-step sx sy sz: Step size (voxel spacing in mm) along each dimension. Default: 2 2 2.
-xstep value: Step size along the X dimension. Default: 2.
-ystep value: Step size along the Y dimension. Default: 2.
-zstep value: Step size along the Z dimension. Default: 2.
-start ox oy oz: Start point (origin) along each dimension. Default: 0 0 0.
-xstart value: Start point along the X dimension. Default: 0.
-ystart value: Start point along the Y dimension. Default: 0.
-zstart value: Start point along the Z dimension. Default: 0.

Data type options

-byte: Write out byte data (default).
-short: Write out short integer data.
-long: Write out long integer data.
-float: Write out single-precision floating-point data.
-double: Write out double-precision floating-point data.
-signed: Write signed integer data.
-unsigned: Write unsigned integer data (default).
-labels: Integer operation on labels.
-discrete: Synonym for -labels.
-continuous: Continuous operation, opposite of -labels.
-voxel_range min max: Valid voxel range for output data.
-real_range min max: Valid real range for output data.

General options

-clobber: Overwrite the output file if it already exists.
-no_clobber: Do not overwrite the output file (default).
-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

Create a default rectangular phantom:

make_phantom phantom.mnc

Create an ellipsoidal phantom centered at (100, 100, 100):

make_phantom -ellipse -center 100 100 100 phantom.mnc

Create a high-resolution phantom with 1mm voxels:

make_phantom -step 1 1 1 -nelements 256 256 256 phantom.mnc

AUTHOR

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