volume_gtc_similarity

Calculate generalized Tanimoto coefficient and overlap metrics for discrete labels.

volume_gtc_similarity [options] <input1.mnc> <input2.mnc>

DESCRIPTION

volume_gtc_similarity calculates the generalized Tanimoto coefficient (GTC) and other overlap metrics between two discrete label volumes. The method is based on Crum, Camara, and Hill (2006), “Generalized Overlap Measures for Evaluation and Validation in Medical Image Analysis” (IEEE Transactions on Medical Imaging).

The tool computes per-label and aggregate similarity metrics, useful for evaluating segmentation accuracy against a reference.

OPTIONS

--background

Include the background label (label 0) in the similarity computation.

--gkappa

Compute the generalized kappa statistic.

--gtc

Compute the generalized Tanimoto coefficient.

--akappa

Compute the average kappa statistic across labels.

--csv

Output results in CSV format.

--exclude l1[,l2,…]

Exclude the specified labels from the computation.

--include l1[,l2,…]

Include only the specified labels in the computation.

EXAMPLES

Compute GTC between two label volumes:

volume_gtc_similarity --gtc labels_auto.mnc labels_manual.mnc

Compute generalized kappa in CSV format:

volume_gtc_similarity --gkappa --csv labels_auto.mnc labels_manual.mnc

Compute metrics excluding labels 0 and 4:

volume_gtc_similarity --gtc --exclude 0,4 labels_auto.mnc labels_manual.mnc

AUTHOR

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

COPYRIGHTS

Copyright © 2011 by Vladimir S. Fonov

SEE ALSO

volume_similarity, fuzzy_volume_similarity