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

By E. Gronenschild, Petra Habets, Heidi I. L. Jacobs, R. Mengelers, N. Rozendaal, J. van Os, M. Marcelis. PLoS ONE, 2012

372 citations recorded by the source corpus.

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.

Subfields: Cognitive Neuroscience, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/5450f3ed7567e526de4094f2a113a297e86ce3fc

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Citations in the corpus

101 Labeled Brain Images and a Consistent Human Cortical Labeling Protocol (2012, background): “Since it has been demonstrated recently that FreeSurfer results can vary depending on software version, operating system, and hardware (Gronenschild et al., 2012), every group of subjects was processed by FreeSurfer with the same computer setup.”
The secret lives of experiments: Methods reporting in the fMRI literature (2012, positive): “However, in at least one case, choices of software versionmay exert substantial effects on research outcomes: Gronenschild et al. (2012) recently demonstrated that different versions of the FreeSurfer library yield significantly different estimates of cortical thickness.”
Structural brain development between childhood and adulthood: Convergence across four longitudinal samples (2016, background): “While it has been shown that different operating systems and workstations can impact FreeSurfer's brain volume estimates (Gronenschild et al., 2012), these effects are generally small and it is not known whether they affect longitudinal change trajectories.”
Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements (2014, methodology): “Given the documented variability in FreeSurfer results with version and operating system (Gronenschild et al., 2012) (as we would expect with our own ANTs pipeline), all data were processed using the same ANTs and FreeSurfer versions on the same hardware platform.”
Image processing and Quality Control for the first 10,000 brain imaging datasets from UK Biobank (2017, background): “Having a fixed acquisition protocol and a core processing pipeline in UK Biobank is a key feature of this project (Gronenschild et al., 2012; Glatard et al., 2015).”