mincmorph
perform morphological operations on MINC volumes
mincmorph [options] <in.mnc> <out.mnc>
DESCRIPTION
mincmorph performs mathematical morphology operations on MINC volumes. Supported operations include erosion, dilation, median dilation, opening, closing, low-pass and high-pass filtering, convolution, distance transform, and connected component grouping. Operations can be applied individually or composed in sequence using the -successive option with single-character operation codes. Several structuring element kernels are available, including 2D 4-connected, 2D 8-connected, 3D 6-connected (default), and 3D 26-connected, or a custom kernel file can be specified.
OPTIONS
-filetype- Use the input file type for the output.
-byte- Store output with 8-bit integer voxels.
-short- Store output with 16-bit integer voxels.
-int- Store output with 32-bit integer voxels.
-float- Store output with 32-bit floating point voxels.
-double- Store output with 64-bit floating point voxels.
-signed- Store output with signed integer voxels.
-unsigned- Store output with unsigned integer voxels.
-2D04- Use a 2D 4-connected structuring element.
-2D08- Use a 2D 8-connected structuring element.
-3D06- Use a 3D 6-connected structuring element (default).
-3D26- Use a 3D 26-connected structuring element.
-kernel <file.kern>- Use a custom kernel file as the structuring element.
-floor- Set the lower threshold for foreground/background classification.
-ceil- Set the upper threshold for foreground/background classification.
-range- Set a range of values for foreground/background classification.
-foreground- Set the foreground output value (default: 1).
-background- Set the background output value (default: 0).
-binarise- Binarise the volume using the foreground/background thresholds.
-clamp- Clamp voxel values to the specified range.
-pad- Pad the volume with background values.
-erosion- Perform morphological erosion.
-dilation- Perform morphological dilation.
-median_dilation- Perform median dilation.
-open- Perform morphological opening (erosion followed by dilation).
-close- Perform morphological closing (dilation followed by erosion).
-lowpass- Apply a low-pass filter using the structuring element.
-highpass- Apply a high-pass filter using the structuring element.
-convolve- Convolve the volume with the structuring element.
-distance- Compute the distance transform.
-group- Label connected components.
-successive <string>- Apply a sequence of operations specified by single-character codes: B (binarise), K (clamp), P (pad), E (erosion), D (dilation), M (median dilation), O (open), C (close), L (lowpass), H (highpass), X (convolve), F (distance/feature), G (group), R (read kernel), W (write), I (invert).
EXAMPLES
mincmorph -erosion input.mnc eroded.mnc
mincmorph -3D26 -dilation input.mnc dilated.mnc
mincmorph -successive BEDD input.mnc result.mnc
mincmorph -kernel custom.kern -close input.mnc closed.mnc
AUTHOR
Andrew Janke - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.
COPYRIGHTS
Copyright © 2000 by Andrew Janke