I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional).

I got the T1 and Flair for this. I registered flair to t1 for every patient.

My manual lesion masks are on DIR imaging. I am using FSL for registration. When I try to register my manual mask to new mask created by freesurfer samseg, fsl couldn't recognize the lesions.mgz extension.

Or should I use t1 space for registration? i tried that one. and then, my registration result was really bad.

As a consequence, ho should we deal with mask registration?

Best,

Dilek