How do I run FIRST? When I load the FSL module FIRST does not pop up as an option and I'm not sure what command to use to even open FRIST up? Am I simply typing in run_first_all and then specifying my -i and -o? This is where I'm stuck, I don't even know where to go to run this. I tried downloading FSL 6.0.4 as well but still did not work. Can you help with that?
Hi Michael, Yes, you are correct in that registering an atlas mask to the native space can yield a Thalamus (or other structures) mask, as this is the main motivation for "FIRST." However, the problem is that this approach relies solely on the information included in the nonlinear registration to reconstruct the subcortical structures, and therefore it would likely lose a lot of individual variances in the process. The biggest benefit with FIRST, in my opinion, is that using this shape analysis you can reconstruct the structures while keeping more of the individual variation. Also, it can also be useful with vertex analysis, which is not straightforward with a volumetric mask.
