I was hoping someone would be able to shed some light on an issue I have been having concerning the volumetric data calculated by FreeSurfer (version 5.3) using the asegstats output file. For information purposes, I am currently using the following command line: recon-all –I [path] –s –sd [Path] –segmentation –all.

I have noticed some differences in the volumetric outputs from a scan I ran on a Linux computer (ubuntu kernal version 3.13.0-85) and the same scan ran on a Mac OS version 10.10.5. These differences in volume range from 5.2-639.4. I have been having difficulty in finding the source of this discrepancy. Are discrepancies commonly found? Could the different computers and operating systems be the reason for these discrepancies? 

I really appreciate your time and assistant with this issue.

Thank you in advance for your help!

Tamara