Hi,

I was wondering if it is possible for me to use FreeSurfer's subcortical segmentation feature with T2-weighted images. Our lab was hoping to make our own T2-weighted Aseg atlas (which I believe is possible with FreeSurfer) and run the subcortical segmentation using that atlas. However, since FreeSurfer is designed for T1-weighted images, I wasn't sure if it be possible to pass a T2w MRI image instead. We don't need any of the other features available from FreeSurfer, just the subcortical segmentation. Would doing this step for T2 MRI be feasible using FreeSurfer?

Thanks,