Thanks Bruce. Another question, since " -no segmentation " flag skips the white matter segmentation step of recon-all. Can I also use the same logic as the "-noskullstrip" flag to replace the wm.seg.mgz file? That's, run " recon-all -autorecon1 -autorecon2 -nosegmentation -s subjid ". Then copy/convert my already segmented brain and name it wm.seg.mgz. After that, treat it as if I had freesurfer's wm.seg.mgz and finally, run " recon-all -autorecon3 -s " to complete the process. What do you think? Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Friday, November 4, 2016 10:50 AM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] Fw: recon-all steps question 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.
