Hi Sourena

the pial surface generation is pretty close to the end of recon-all, so you are probably better off just running the whole thing

cheers Bruce On Sun, 18 Aug 2013, Sourena Soheili-Nezhad wrote:

Hello Freesurfer community

I am trying to perform a voxelwise longitudinal analysis (outside FS). I have been searching for brain extraction algorithms and it seems that Freesurfer provides the most accurate solution. If the primary objective is highest accuracy, should I use recon-all products proximal to surface generation (e.g. brain.mgz), or it would be wiser to further proceed to surface generation?

Could someone advise me how to stop the recon-all at an optimal step?

Cheers, Sourena Soheili-Nezhad