Journal Article

The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements

Jacobs, Heidi I. L., Mengelers, Ron, Habets, Petra, Rozendaal, Nico, van Os, Jim, Gronenschild, Ed H. B. M., Marcelis, Machteld

2012

Overview

FreeSurfer is a popular software package to measure cortical thickness and volume of neuroanatomical structures. However, little if any is known about measurement reliability across various data processing conditions. Using a set of 30 anatomical T1-weighted 3T MRI scans, we investigated the effects of data processing variables such as FreeSurfer version (v4.3.1, v4.5.0, and v5.0.0), workstation (Macintosh and Hewlett-Packard), and Macintosh operating system version (OSX 10.5 and OSX 10.6). Significant differences were revealed between FreeSurfer version v5.0.0 and the two earlier versions. These differences were on average 8.8 ± 6.6% (range 1.3-64.0%) (volume) and 2.8 ± 1.3% (1.1-7.7%) (cortical thickness). About a factor two smaller differences were detected between Macintosh and Hewlett-Packard workstations and between OSX 10.5 and OSX 10.6. The observed differences are similar in magnitude as effect sizes reported in accuracy evaluations and neurodegenerative studies.The main conclusion is that in the context of an ongoing study, users are discouraged to update to a new major release of either FreeSurfer or operating system or to switch to a different type of workstation without repeating the analysis; results thus give a quantitative support to successive recommendations stated by FreeSurfer developers over the years. Moreover, in view of the large and significant cross-version differences, it is concluded that formal assessment of the accuracy of FreeSurfer is desirable.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Adolescent / Adult / Alzheimer's disease / Alzheimers disease / Anatomy / Automation / Biology / Cerebral Cortex - anatomy & histology / Computer Science / Computers / Consent / Cortex / Data processing / Dementia / Humans / Huntingtons disease / Macintosh personal computers / Magnetic resonance imaging / Magnetic Resonance Imaging - methods / Mathematics / Medicine / Mental health / Middle Aged / Morphology / Neuropsychology / Neurosciences / Operating systems / Organ Size / Psychiatry / Psychosis / Reliability aspects / Scanners / Science Policy / Software / Studies / Thickness measurement / Work stations / Workstations / Young Adult