mri_compute_seg_overlap - compute coefficents of overlap
mri_compute_seg_overlap [<options>] segvol1 segvol2
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).
| Argument | Explanation |
|---|---|
| segvol1 | first segmentation volume |
| segvol2 | second segmentation volume |
| Argument | Explanation |
|---|---|
| -log filename | log file for individual Dice (12 structure pairs, plus mean, std, and 'overall') |
| -mlog filename | log file for mean Dice |
| -slog filename | log file for std Dice |
| -olog | log file for 'overall' Dice (mean excluding wm, gm and accumbens) |
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.
Report bugs to <freesurfer@nmr.mgh.harvard.edu>