[Freesurfer] Incorporating (high resolution) T2- and FLAIR volumes

Hi FreeSurfer experts!

We have isotropic T1/T2 and FLAIR volumes for a larger cohort. It would be fine to use the T2 / FLAIR volumes to improve the segmentation and to perform a couple additional analyses using FS. This leads to the following questions:

1) How do I incorporate T2/Flair volumes into the recon all processing stream?

a) Would it be like: recon-all bert -all -T2 /luke/xyz/007-T2.nii ?

b) What is expected to get the better results regarding the pial surface: FLAIR or T2? (both are at 1x1x1mm)

2) Is there any module in FS to detect white matter lesions?

3) How can I perform myelin mapping using the ratio method (T1w/T2w)? Or do I have to switch to Caret?

Many thanks in advance for your help and advice!

Best wishes,

Luke