ibsr gm/wm segmentation very inaccurate

[michaelmcl1960]

I have used both CAT12 (CAT12.8.2 r2170) and Freesurfer to segment a particular brain scan and I get completely different volumes.

<
                        CAT12 from ibsr   Freesurfer 7.3.2
 Left Cerebral WM(cc):           209        242
 Left Cerebral Cortex (cc)       444        269
 Left Lateral Ventricle (cc):     28         43
 Right Cerebral WM (cc):         208        242
 Right Cerebral Cortex (cc):     440        270 
 Right Lateral Ventricle (cc):    20         28
 ----------------------------------------------
 Total                          1350       1095
>
 Total brain volume (cc):       1618       1309

As we can see from the image, CAT12 overestimates the GM and under estimates the WM and ventricles and yet the volume of the CAT12 pial surface is 1080 cc which is in good agreement with Freesurfer. The CAT12 volumes are calculated from the ibsr output file.

[michaelmcl1960]

Actually I need also to take probability map into the calculation so this is not a problem.