Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

2017-02-08 Thread
> >recon-all -autrecon-pial -s -sd > >note that it is NOT autorecon2-pial, but just autorecon-pial (leave out the >'2') > >cheeers >Bruce > > >On Thu, 9 Feb 2017, 冉倩 wrote: > >> Hi Bruce, >> If I use brain.finalsurfs, then I run recon-

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

2017-02-08 Thread
ine if you are just rerunning the pial. Edit brainmask if you are starting earlier so all the downstream volumes including brain.finalsurfs will have the dura removed Cheers Bruce On Feb 7, 2017, at 10:45 PM, 冉倩 wrote: brain.finalsurfs.mgz? not brainmask.mgz? or brain.finalsurfs.mgz for pi

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

2017-02-07 Thread
7 10:37 PM, 冉倩 wrote: Hi Prof.Douglas Greve, Yes, probematic surface normally existed near supeiror dura ( aroun superior frontal lobe or parietal lobe or central gry area). Just now I am confused about the next steps. If I manually erase ( whether I can modfiy control point just like modi

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

2017-02-07 Thread
can use it to automatically correct this type of problem. Or you can erase the dura in those regions on the brainmask.mgz and recreate the pial surface cheers Bruce On Wed, 8 Feb 2017, 冉倩 wrote: Hi Bruce, Thanks for your reply. [IMAGE] For this, I think pial surface (the location where I c

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

2017-02-07 Thread
on the brainmask.mgz and recreate the pial >surface > >cheers >Bruce > > > >On Wed, 8 Feb 2017, 冉倩 wrote: > >> Hi Bruce, >> Thanks for your reply. >> >> [IMAGE] >> For this, I think pial surface (the location where I circle) already >>