itk_morph

perform binary morphological image operations (dilate, erode, open, close)

itk_morph <input> <output> [options]

DESCRIPTION

itk_morph applies binary morphological operations to a volume using the Insight Toolkit (ITK). Operations are specified through an expression string (--exp) composed of single-character operation codes. Multiple operations can be chained in sequence within a single expression, and each operation uses the structuring element radius set by --radius.

The input image is first binarized using either a fixed threshold (--threshold) or automatic bimodal threshold estimation (--bimodal). The supported operations are: D (dilate), E (erode), M (median filter), T (binary thinning), P (pruning), I (inversion), S (threshold / binarize), and A (add / union with the original input). Combining these operations allows standard compound operations such as morphological opening (ED) and closing (DE).

OPTIONS

--verbose

Print verbose information during processing.

--clobber

Overwrite the output file if it already exists.

--exp str

Specify the morphological expression string. Operation codes: D = dilate, E = erode, M = median, T = thin, P = prune, I = invert, S = threshold/binarize, A = add (union with original).

--bimodal

Use bimodal (Otsu) threshold estimation to automatically binarize the input before applying morphological operations.

--threshold val

Set a fixed threshold value for binarizing the input image. Voxels above this value are set to 1; all others are set to 0.

--radius r

Set the radius (in voxels) of the structuring element used for morphological operations. Default is 1.

EXAMPLES

Erode a binary mask with a radius of 2:

itk_morph mask.mnc eroded.mnc --exp E --radius 2

Dilate then erode (morphological closing):

itk_morph mask.mnc closed.mnc --exp DE --radius 1

Apply automatic thresholding followed by dilation:

itk_morph input.mnc output.mnc --bimodal --exp D --radius 3

Erode then dilate (morphological opening) with a fixed threshold:

itk_morph input.mnc output.mnc --threshold 0.5 --exp ED --radius 1

Invert a binary mask:

itk_morph mask.mnc inverted.mnc --exp I

AUTHOR

Vladimir S. Fonov - Montreal Neurological Institute, McGill University.

COPYRIGHTS

Copyright (C) Vladimir S. Fonov, McConnell Brain Imaging Centre, McGill University.

SEE ALSO

itk_g_morph, mincmorph, itk_distance, minccalc