All,
Our lab is working with longitudinal (two time points) data from a cohort of around 130 individuals. We are attempting to make comparisons between time points 1 and 2 on measures like total brain volume, ventricular volume, ventricle-brain-ratio, and cortical thickness. However, we have run into an issue--we are seeing net increases in cortical thickness and total brain volume over time (which seems biologically implausible, given our age range of ~30-60 yrs old). We think it may have something to do with the fact that the T1w data from each time point was acquired with slightly different parameters and on different scanners, possibly leading to a rounding error in quantification of volumes/thickness. Timepoint 1 data are 1.0mm isotropic and were acquired on a 3T Siemens Tim Trio with 12ch headcoil. Timepoint 2 data are 0.8mm isotropic and were acquired on the same scanner, but which went through an upgrade to a Prisma Fit between timepoints, using a 32ch coil.
Currently we have been comparing data from the cross sectional stream. We would like to use the longitudinal stream if that would improve results, but we saw this post that cautioned against it: https://www.mail-archive.c om/freesurfer@nmr.mgh.harvard.edu/msg52992.html
What would be your recommendation for comparing this data longitudinally? Any thoughts on why we are seeing net increases in volume/thickness, and how to avoid that? One idea we had was perhaps degrading each image by rigid co-registration and then bringing each image into the halfway space between the two (as FSL's SIENA does).
Thanks,
James