NAME

mri_compute_seg_overlap - compute coefficents of overlap

SYNOPSIS

mri_compute_seg_overlap [<options>] segvol1 segvol2

DESCRIPTION

This program compares two segmentation volumes and computes the Dice and Jaccard Coefficients. It considers 12 major structures (label numbers):
L/R Hippocampus (17,53)
L/R Caudate (11,50)
L/R Putamen (12,51)
L/R Pallidum (13,52)
L/R Amygdala (18,54)
L/R Thalamus_Proper (10,49)
L/R Lateral_Ventricle (75,76)
Third and Fourth Ventricles (14,15)
L/R Inf_Lat_Vent (5,44)
L/R Cerebral_White_Matter (2,41)
L/R Cerebral-Cortex (3,42)
L/R Accumbens-area (26,58)

NOTE! white matter, cortex and accumbens are excluded from the
'overall Dice' measure (which is a mean), as the surface-based
wm/gm measures are more accurate (and accumbens is very
difficult to measure).

POSITIONAL ARGUMENTS

ArgumentExplanation
segvol1first segmentation volume
segvol2second segmentation volume

REQUIRED-FLAGGED ARGUMENTS

None

OPTIONAL-FLAGGED ARGUMENTS

ArgumentExplanation
-log filenamelog file for individual Dice
(12 structure pairs, plus mean, std, and 'overall')
-mlog filenamelog file for mean Dice
-slog filenamelog file for std Dice
-ologlog file for 'overall' Dice
(mean excluding wm, gm and accumbens)

EXAMPLE 1

mri_compute_seg_overlap manual_seg.mgz aseg.mgz

Used to compare the quality of the automatic segmentation with a manual segmentation. A Dice of 0.85 is about average.

REPORTING

Report bugs to <freesurfer@nmr.mgh.harvard.edu>