itk_merge_labels

Merge multiple probability maps into a single label image by maximum probability voting.

itk_merge_labels i input_i.mnc [j input_j.mnc ...] <output.mnc>

DESCRIPTION

itk_merge_labels combines multiple probability map volumes into a single discrete label image. Each input consists of a label number paired with a probability map volume. At each voxel, the label with the highest probability is assigned to the output.

This tool is typically used after probabilistic segmentation or patch-based classification to produce a final hard segmentation from a set of per-class probability maps. Input pairs can also be specified via a CSV file.

OPTIONS

--csv input

Read label-number and probability-map pairs from a CSV file instead of the command line. Each row should contain a label number and a file path.

--clobber

Overwrite the output file if it already exists.

--byte

Store output voxels as unsigned byte.

--short

Store output voxels as short integer.

EXAMPLES

# Merge three probability maps into a label image
itk_merge_labels 1 prob_csf.mnc 2 prob_gm.mnc 3 prob_wm.mnc output.mnc

# Merge using a CSV file
itk_merge_labels --csv label_list.csv output.mnc

# Store result as byte
itk_merge_labels 1 prob_csf.mnc 2 prob_gm.mnc 3 prob_wm.mnc \
    output.mnc --byte

AUTHOR

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

COPYRIGHTS

Copyright © 2009-2024 by Vladimir S. Fonov

SEE ALSO

itk_merge_discrete_labels , itk_split_labels