Dear member of the list,

I've compared the output of mri_compute_seg_overlap (FS 5.1.0 and 5.3.0) against an home-made script to calculate the DICE coefficients between two asg.mgz files.

The results ranges from being perfectly equal (e.g. label 58) up to an error at the second decimal place (e.g. label 42), which is not acceptable.

Where do you think is the origin of these inconsistencies?

Here's the complete result of the test:

     freesurfer    VS    python script
label 2 = 0.975814      label 2 = 0.975759
label 41 = 0.980171     label 41 = 0.980135
label 3 = 0.980298      label 3 = 0.961283
label 42 = 0.983296     label 42 = 0.965541
label 4 = 0.979572      label 4 = 0.979572
label 43 = 0.975789     label 43 = 0.975789
label 17 = 0.950502     label 17 = 0.942725
label 53 = 0.953055     label 53 = 0.945481
label 10 = 0.983729     label 10 = 0.983117
label 49 = 0.988228     label 49 = 0.987909
label 11 = 0.97027      label 11 = 0.970270
label 50 = 0.952635     label 50 = 0.952635
label 12 = 0.974187     label 12 = 0.974187
label 51 = 0.976775     label 51 = 0.976775
label 13 = 0.972107     label 13 = 0.972107
label 52 = 0.981569     label 52 = 0.981568
label 18 = 0.921979     label 18 = 0.920228
label 54 = 0.95705      label 54 = 0.950452
label 26 = 0.887918     label 26 = 0.887918
label 58 = 0.9501       label 58 = 0.950100
label 14 = 0.973062     label 14 = 0.971466
label 15 = 0.963786     label 15 = 0.960308
label 5 = 0.897959      label 5 = 0.897959
label 44 = 0.926717     label 44 = 0.924583

The core of the home-made python script is:

import numpy as np
import nibabel as nib

# usage: DICE('pathToAseg1.mgz','pathToAseg1.mgz',label)

def DICE(dataPathX,dataPathY,label=1):
    # X and Y must be binary images
    # or specify label to be used (e.g LeftHippocampus=17)
    imageX = nib.load(dataPathX)
    imageY = nib.load(dataPathY)
    X = (imageX.get_data()==label).astype(float)
    Y = (imageY.get_data()==label).astype(float)
    VolX = X.sum()
    VolY = Y.sum()
    XY = (X*Y).sum() # X*Y prod element by elements. XY=volume of intersection
    diceXY = 2.0 * XY / (VolX + VolY)
    return diceXY

Best regards,

Luigi Antelmi