1a) You would do this after running recon-all on the T1-weighted image. It
will only adjust the surfaces, not the segmentation. Something like
recon-all -T2pial path to flair
1b) this will work with either, but in my experience the FLAIR helps more
to distinguish dura from gm
2) Yes. The
I find the T2w image works well for removing dura and blood vessels, but
I'm not sure FLAIR would work for T1w/T2w myelin mapping because of what
would happen to the ratio near the pial surface.
Instructions for T1w/T2w myelin mapping are available here:
