[Freesurfer] Two Inquiries

1. Segmentation of partial brain

Dear FreeSurfers,

1. Can I expect recon-all to work on a T1W image where only part of the brain is in FOV? The obvious answer is that I should just try, but it would help to know in case I get unexpected results. Perhaps a more appropriate question is: what should I expect to work and what should I expect to fail.

Thank you,

---------------------- 2. Rotated segmentation

Dear FreeSurfers,

I start with a T1W image in NIFTI format. After running recon-all, I use mri_convert to convert aseg.mgz to aseg.nii. This aseg.nii image does not overlay the original T1W. It is slightly rotated. Is it normal? If I would like to make it overlay what should I do? Register using flirt?

Thank you,