mri_overlap
This page proposes a new program, called mri_overlap, that will replace the redundant (and buggy) mri_compute_seg_overlap and mri_compute_overlap. A primary new feature is the ability to save a detailed overlap report to a JSON file.
USAGE: mri_overlap <vol1> <vol2> [options] DESCRIPTION: This program computes the overlap between two segmentation volumes. The following statistics can be calculated for each label: dice coefficient - ... jaccard coefficient - ... volume difference - ... By default, only dice scores are computed, but this can be reconfigured with the --measures flag. Each structure in the input volumes will be considered by default, but an alternative list of labels can be specified with the -l flag. Additionally, the --seg flag will compute the overlap between the following 12 major anatomical structures: Hippocampus (17,53) Caudate (11,50) Putamen (12,51) Pallidum (13,52) Amygdala (18,54) Thalamus Proper (10,49) Lateral Ventricle (4,43) Third and Fourth Ventricles (14,15) Inf Lateral Vent (5,44) Cerebral White Matter (2,41) Cerebral Cortex (3,42) Accumbens Area (26,58) OPTIONAL ARGUMENTS: -o, --out Save detailed overlap report to a JSON file. -m, --measures List of measures to compute. By default, only dice scores are computed. Options include: dice, jaccard, voldiff -l, --labels Space-separated list of labels to use. By default, the overlap will be computed between all labels available in both input volumes. -f, --labelfile File with space-separated list of labels to use. -s, --seg Compute overlap between the major segmentation structures listed above.
The proposed JSON output would look something like this:
{ "names": { "1": "structure 1", "2": "structure 2" ... }, "inputs": [ "/path/to/manual_label.mgz", "/other/path/to/aseg.mgz" ], "measures": { "dice": { "mean": 0.9142, "std": 0.0232, "labels": { "2": 0.9143, "3": 0.8739, "4": 0.9002, ... } }, "jaccard": { "mean": 0.8902, "std": 0.0144, "labels": { "2": 0.8921, ... } }, "voldiff": { "mean": 0.0221, "std": 0.0032, "labels": { "2": 0.0123, ... } } } }