Reproducibility of brain tissue volumes in longitudinal studies: Effects of changes in signal-to-noise ratio and scanner software

It is imperative that users of voxel-based morphometry (VBM) be aware of its reproducibility and the factors which influence results. We assessed the reproducibility of a VBM software package (SPM5) in measuring gray matter (GM) and white matter (WM) volumes from at least two consecutive 3D T1-weighted studies in 64 subjects. Factors investigated were the inter-study interval (ISI: 2.2 h to 124 days), signal-to-noise ratio (SNR: number of image averages (NA) = 1 or 2), scanner software version and idle time. SNR was measured by direct estimation of tissue noise (SNRTN) and mean intensity in noise-only voxels (SNRNO). After the scanner software upgrade, voxel intensity increased 5-fold and WM mean SNRTN by 24% (p < 0.001). Mean WM and GM volume changes in consecutive studies were near 0% (absolute SD of 7 ml and 10 ml respectively). Studies acquired with original scanner software showed a small (1.6%) mean GM volume increase attributed to SNRTN increases in five subjects due to scanner maintenance. GM volumes increased with SNRTN across the software upgrade (up to 4.3%; p < 0.01) and NA = 2 acquisitions (up to 4.1%; p < 0.001). GM and WM volumes were independent of ISI when ISI did not encompass the software change. Scanner idle times of > 6 h decreased SNR by 7% (p < 0.001). SPM5 failed to include visible peripheral GM in only 2 subjects. SNRTN increases were greater than SNRNO increases across the software upgrade. It was concluded that SNR changes significantly influence SPM5-derived GM volumes. SNR may be influenced by scanner software upgrades and hardware condition and should be routinely assessed in studies of brain volume.