Abstract
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.
Highlights
No differences were detected between repeated single runs nor between single runs and parallel runs on the same workstation and for the same FreeSurfer and operating system (OS) version
Since we did not find any differences between OSX 10.6.4 and OSX 10.6.5, we will use the terms OSX 10.5 and OSX 10.6 for OSX 10.5.8 and OSX 10.6.4/5, respectively
The differences are presented in more detail below, starting with an overview and subsequently zooming in on specific structures and data processing comparisons
Summary
A number of reported studies discussed the accuracy of the technique by comparing the volume of specific brain structures, such as the hippocampus or amygdala, with manually derived volumes [2,3,4,5]. The reliability of the measurements was subject of a number of investigations. Some of these studies addressed the effect of scanner-specific parameters, including field strength, pulse sequence, scanner upgrade, and vendor (cortical thickness: [9,10]; volume: [11]). It has been shown that Freesurfer is capable of reliably capturing (subtle) morphological and pathological changes in the brain (e.g., [5,13])
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