lmer set-up (t-test with covariate?) ?

I have 139 subjects (ID), with measurements taken at two time points (Time1, Time2), at 148 brain regions, a dependent measure called volume, and a covariate called thickness.
Each subject has 148 brain regions with volume and thickness measured twice
I am trying to find out if there is a difference in volume between timepoint 1 and timepoint 2 while controlling for thickness. I want to know which brain regions show this difference. I need help setting up the model. Specifically the timepoint part is throwing me off...
I am using R. and trying to figure out a model with linear mixed models with (1|ID) as random factor, fixed factors regions, thickness.