Hi Paul
we required the T1.mgz, brainmask.auto.mgz and brainmask.mgz volumes so must create them somehow. I think if you copy/convert your already-stripped and name it brainmask.mgz we should treat that as if you had edited our skull stripping and you should be able to run from their forward (autorecon2 and autorecon3 I believe)
cheers Bruce On Fri, 4 Nov 2016, miracoo...@gmail.com wrote:
Please can someone answer this. Thanks " 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: miracoo...@gmail.com Sent: Wednesday, November 2, 2016 9:39 AM To: Freesurfer support list Subject: Fw: recon-all steps question Sent from my BlackBerry 10 smartphone. From: miracle ozzoude <miracoo...@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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.