Re: [Freesurfer] FW: registration difficulty

2014-04-04 Thread Douglas N Greve
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 02 April 2014 22:35 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: registration difficulty should I now rerun the bbregsiter

Re: [Freesurfer] FW: registration difficulty

2014-04-03 Thread Erik O'Hanlon
: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 02 April 2014 22:35 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: registration difficulty should I now rerun the bbregsiter and create

Re: [Freesurfer] FW: registration difficulty

2014-04-03 Thread Erik O'Hanlon
...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 03 April 2014 10:23 To: Freesurfer support list Subject: Re: [Freesurfer] FW: registration difficulty Hi Doug, Thanks for that, I will give that a shot and see how it looks. As for my highres hippo images, I ran

[Freesurfer] FW: registration difficulty

2014-04-02 Thread Erik O'Hanlon
Dear FS experts, I am running my first FS analysis and I'm trying to register my hippocampal subdivision volumes to my diffusion space image but cannot get good alignment. I ran my diffusion preprocessing in ExploreDTI so don't have the register.dat file automatically so created this using

Re: [Freesurfer] FW: registration difficulty

2014-04-02 Thread Bruce Fischl
Hi Erik so you had a separate (presumably highres) acquisition within the hippocampus? Have you registered that with bbregister? Your best bet is probably doing so, then composing the two registrations (and inverting one, depending on what direction you want to go). cheers Bruce On Wed, 2

Re: [Freesurfer] FW: registration difficulty

2014-04-02 Thread Erik O'Hanlon
MAKE A DIFFERENCE WORLDWIDE From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 02 April 2014 19:58 To: Erik O'Hanlon Subject: Re: [Freesurfer] FW: registration difficulty Hi Erik can you cc the list so that others (like Doug!) can respond? thanks Bruce

Re: [Freesurfer] FW: registration difficulty

2014-04-02 Thread Douglas N Greve
If that is the situation, then you can use the --int flag to bbregister On 04/02/2014 12:19 PM, Bruce Fischl wrote: Hi Erik so you had a separate (presumably highres) acquisition within the hippocampus? Have you registered that with bbregister? Your best bet is probably doing so, then

Re: [Freesurfer] FW: registration difficulty

2014-04-02 Thread Douglas N Greve
Subject: Re: [Freesurfer] FW: registration difficulty Hi Erik can you cc the list so that others (like Doug!) can respond? thanks Bruce On Wed, 2 Apr 2014, Erik O'Hanlon wrote: Hi Bruce, Thanks so much for your reply. As for the specifics of what I have tried, so rry if it was unclear. I