I am new to freesurfer. I would like to know the command for subcortical segmentation of brain MRI volume. I read on freesurfer wiki page the recon-all -autorecon2 stage is useful for this.
My question is what exact command should I use for this purpose. I am familiar with FSL. In FSL 'FIRST' command is useful for this and it gives you segmentaion in approimately 7-10 minutes. But in freesurfer it is written that recon-all -autorecon2 stage can take upto 12 hours for segmentation of one volume. I would like to know if there is any other option for this apart from autorecon2 stage which can give me segmentation in less time.
Also, when I am using recon-all -all option, I am getting segmentation of all the volumes in MNI space wraped using non-linear registration. Is there any way I can get segmentation in original image space??
Thank you for your help.