The FreeSurfer analysis pipeline comprises two main processing streams, a volume-based stream and a surface-based stream. The volume-based stream is designed to assign a neuroanatomical label to each (sub)cortical voxel, whereas the surface-based stream is developed to derive the white and pial surfaces from which, among others, cortical volumes and cortical thickness (CT) are derived. More details can be found in Document S1 and references [2] (link), [17] (link)–[28] (link).
The volumes are presented by FreeSurfer in the form of tables and labeled voxels. The tabulated volumes are more accurate than the voxel volumes because they are corrected for partial volume effects. Both types of volumes were used in our analysis (seeDocument S1 for more details).
In order to compare the results with accuracy results previously reported by Lehmann and colleagues [5] (link), a few white matter and grey matter regions were merged to produce a whole gyrus or lobe (left and right), such as medial-inferior temporal gyrus (MITG), superior temporal gyrus (STG), and temporal lobe (TempL). Simarly, total ventricle volume (Ventr) was constructed (left+right added together). In this manner, a total of 7 composite volumes were assembled. (The respective segmentation labels were kindly provided to us by Dr. Manja Lehmann, University College London, UK, seeDocument S1 for more details).
In total, we computed 190 (sub)cortical volumes (185 for v5.0.0) and 68 CT values. It should be noted that no manual corrections were made to any of the FreeSurfer results in order to ensure a valid analysis. However, a visual inspection was performed to check the segmentations.
Three versions of FreeSurfer were used: v4.3.1, released on 19 May 2009, version v4.5.0, released on 11 August 2009, and version v5.0.0, released on 16 August 2010. For the Mac workstations these are 32 bits versions (due to problems to build some third party libraries in 64 bits mode on the Mac), whereas for the HP workstation these are 64 bits versions.
The volumes are presented by FreeSurfer in the form of tables and labeled voxels. The tabulated volumes are more accurate than the voxel volumes because they are corrected for partial volume effects. Both types of volumes were used in our analysis (see
In order to compare the results with accuracy results previously reported by Lehmann and colleagues [5] (link), a few white matter and grey matter regions were merged to produce a whole gyrus or lobe (left and right), such as medial-inferior temporal gyrus (MITG), superior temporal gyrus (STG), and temporal lobe (TempL). Simarly, total ventricle volume (Ventr) was constructed (left+right added together). In this manner, a total of 7 composite volumes were assembled. (The respective segmentation labels were kindly provided to us by Dr. Manja Lehmann, University College London, UK, see
In total, we computed 190 (sub)cortical volumes (185 for v5.0.0) and 68 CT values. It should be noted that no manual corrections were made to any of the FreeSurfer results in order to ensure a valid analysis. However, a visual inspection was performed to check the segmentations.
Three versions of FreeSurfer were used: v4.3.1, released on 19 May 2009, version v4.5.0, released on 11 August 2009, and version v5.0.0, released on 16 August 2010. For the Mac workstations these are 32 bits versions (due to problems to build some third party libraries in 64 bits mode on the Mac), whereas for the HP workstation these are 64 bits versions.
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