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

CAT12 (cc) Freesurfer 7.3.2 (cc)
Left Cerebral White Matter volume(cc): 209  Left hemisphere cerebral white matter volume 242
Left Cerebral Cortex volume(cc): 444  Left hemisphere cortical gray matter volume 269
Left Lateral Ventricle volume(cc): 28 Left-Lateral-Ventricle 43
Right Cerebral White Matter volume(cc): 208  Right hemisphere cerebral white matter volume 242
Right Cerebral Cortex volume(cc): 440  Right hemisphere cortical gray matter volume 270
Right Lateral Ventricle volume(cc): 20 Right-Lateral-Ventricle 28
Total 1350 Total 1095
Total volume (cc): 1618.09  Brain Segmentation Volume 1309
 Estimated Total Intracranial Volume 1852

What could be causing this difference?

The brain scan was done with MPRAGE protocol with 176x256x256 voxels of size 1mmx0.976mmx0.976mm

Which one is correct?

The scan is of a normal adult male aged 62 with chronic migraine.

Michael McLaughlin,