I have been playing around with the new beta version, and am very interested in the -FLAIRpial option. I have been using this successfully on cross-sectional runs, but would like to extend it to cross sectional runs.

I have played around with trying to get this to work, including copying FLAIRconf.mgz to the longitudinal run directions (subjid.long.template) and the recon-alll -long command with -FLAIRpial. Although this runs, it produces cortical thickness estimates that appear underestimated on visual inspection.

Is there a better way to incorporate -FLAIRpial on longitudinal runs? Is it even possible at this stage?