itk_split_labels

Split discrete label volume into per-label probability volumes with anti-aliasing.

itk_split_labels <input> <output_XXXX.mnc> [options]

DESCRIPTION

itk_split_labels splits a discrete label volume into separate per-label volumes. The output filename must contain a printf-style format specifier (e.g., XXXX or %04d) which is replaced by the label number for each output file.

By default, the tool produces binary masks for each label. When anti-aliasing is enabled (--aa), the label boundaries are smoothed to produce continuous probability maps rather than hard binary masks, which is useful for subsequent interpolation or probabilistic analysis. Optional Gaussian blurring and expit (logistic) sharpening can be applied to the probability maps.

Labels can be remapped using a lookup table or relabel file before splitting.

OPTIONS

--clobber

Overwrite output files if they already exist.

--order n

B-spline interpolation order for resampling (default: 2).

--uniformize step

Uniformize the volume to the given step size before splitting.

--unistep step

Set a uniform step size for the output volumes.

--byte

Store output voxels as unsigned byte.

--short

Store output voxels as short integer.

--float

Store output voxels as single-precision floating point.

--relabel map.txt

Relabel input labels according to the mapping in the specified text file.

--lut map.txt

Apply a lookup table from the specified text file.

--lut-string

Interpret the LUT argument as a string rather than a file path.

--aa, --antialias

Enable anti-aliased label splitting to produce smooth probability maps.

--blur fwhm

Apply Gaussian blurring with the specified full-width at half-maximum (mm).

--expit beta

Apply expit (logistic) sharpening with the given beta parameter.

--normalize

Normalize probability maps so they sum to 1.0 at each voxel.

--missing max

Maximum number of missing labels to tolerate.

--layers n

Number of anti-aliasing layers (default: 4).

EXAMPLES

# Split labels into binary masks
itk_split_labels labels.mnc label_%04d.mnc

# Split with anti-aliasing for smooth probability maps
itk_split_labels labels.mnc prob_%04d.mnc --aa --float

# Split with relabelling and normalization
itk_split_labels labels.mnc prob_%04d.mnc --relabel remap.txt \
    --aa --normalize --float

# Split with blurring and expit sharpening
itk_split_labels labels.mnc prob_%04d.mnc --aa --blur 2.0 --expit 5.0

AUTHOR

Vladimir S. Fonov - McConnell Brain Imaging Centre, Montreal Neurological Institute.

COPYRIGHTS

Copyright © 2009-2024 by Vladimir S. Fonov

SEE ALSO

itk_merge_labels , itk_merge_discrete_labels