Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

2012-11-21 Thread Longchuan Li
From: Douglas N Greve To: Longchuan Li Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Wednesday, November 21, 2012 3:20 PM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz Hi Longchuan, I'm still not sure I understand what you are trying to do ult

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

2012-11-21 Thread Douglas N Greve
--- > *From:* Douglas N Greve > *To:* Longchuan Li > *Cc:* "freesurfer@nmr.mgh.harvard.edu" > ; Bruce Fischl > > *Sent:* Tuesday, November 20, 2012 3:19 PM > *Subject:* Re: [Freesurfer] the positions of white/pial surfaces and > the brain.mgz > > > Hi Longchu

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

2012-11-20 Thread Longchuan Li
_ From: Douglas N Greve To: Longchuan Li Cc: "freesurfer@nmr.mgh.harvard.edu" ; Bruce Fischl Sent: Tuesday, November 20, 2012 3:19 PM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz Hi Longchuan, mris_fill create a volume with a different ge

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

2012-11-20 Thread Douglas N Greve
t; > thank you! > > Longchuan > > PS: I also used "-cm" option in recon-all as suggested by Bruce. I > just got the results and the problem is still there. > > ---------------- > *From:* Douglas N Greve &

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

2012-11-19 Thread Longchuan Li
t;> >> Longchuan >> >> >> ________________ >> >> From: Bruce Fischl >> To: Longchuan Li >> Cc: FreeSurfer >> Sent: Monday, November 19, 2012 8:57 AM >> Subject: Re: [Freesu

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

2012-11-19 Thread Longchuan Li
AM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz use bbregister, something like bbregister --s subjectname --init-fsl --t2 --mov lowb.nii --reg register.dat where lowb is the low b (usually b=0) volume from your DTI, the one that you used as the template for

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

2012-11-19 Thread Douglas N Greve
_ >> >> From: Bruce Fischl >> To: Longchuan Li >> Cc: FreeSurfer >> Sent: Monday, November 19, 2012 8:57 AM >> Subject: Re: [Freesurfer] the positions of white/pial surfaces and the >> brain.mgz >> >&

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

2012-11-19 Thread Bruce Fischl
12 8:57 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz Hi Longchuan have you tried the -cm (conform to min) option in recon-all? cheers Bruce On Sun, 18 Nov 2012, Longchuan Li wrote: > Hi, FreeSurfer experts > > I have a question regarding coregiste

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

2012-11-19 Thread Longchuan Li
Longchuan From: Bruce Fischl To: Longchuan Li Cc: FreeSurfer Sent: Monday, November 19, 2012 8:57 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz Hi Longchuan have you tried the -cm (conform to min) option in recon-all? cheers Bruc

Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz

2012-11-19 Thread Bruce Fischl
Hi Longchuan have you tried the -cm (conform to min) option in recon-all? cheers Bruce On Sun, 18 Nov 2012, Longchuan Li wrote: Hi, FreeSurfer experts I have a question regarding coregistering white and pial surfaces with the brain.mgz and would appreciate your help on this. I am working