Hello Freesurfer,

I have couple of questions. While going through the frequently asked questions on your pagehttp://freesurfer.net/fswiki/UserContributions/FAQ I came across a question regarding how to integrate a skull stripped from another problem into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid ----> create a symbolic link from T1.mgz to brainmask.auto.mgz and another like from brainmask.auto.mgz to brainmask.mgz ------> after run the finall stages of recon-all: recon-all -autorecon2 -autorecon3 -s subjid).

First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created during skull stripping? why are they present if I included the "-no skullstrip" flag?

Second question, where do I insert my already skull stripped data in the symbolic link?

Last question, the final stages of recon-all ( recon-all -autorecon2 -autorecon3) doesn't include skull stripping, how can I be sure my skull stripped data was incorporated into the freesurfer recon-all process?

Best,

Paul

Sent from my BlackBerry 10 smartphone.

From: miracle ozzoude <miracooloz@gmail.com>

Sent: Monday, October 31, 2016 8:39 AM

To: Douglas N Greve

Subject: recon-all steps question

Hello Freesurfer,

I have couple of questions. While going through the frequently asked questions on your page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a question regarding how to integrate a skull stripped from another problem into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid ----> create a symbolic link from T1.mgz to brainmask.auto.mgz and another like from brainmask.auto.mgz to brainmask.mgz ------> after run the finall stages of recon-all: recon-all -autorecon2 -autorecon3 -s subjid).

First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created during skull stripping? why are they present if I included the "-no skullstrip" flag?

Second question, where do I insert my already skull stripped data in the symbolic link?

Last question, the final stages of recon-all doesn't include skull stripping, how can I be sure my skull stripped data was incorporated into the freesurfer recon-all process?

Best,

Paul