Re: [Freesurfer] Autorecon re-processing

2005-09-19 Thread Doug Greve
does your version not tell you these things when you run -help? Fornito, Alexander wrote: HI, Just wanted to check a few things re: re-running autorecon. I'm guessing that re-running autorecon with the -pial flag re-runs make_final_surfaces, which takes about 4-6 hours (correct?). What is

Re: [Freesurfer] anatomical stats

2005-09-19 Thread Doug Greve
what do you mean it does not work? Because things aren't aligned? I'm afraid you're on your own if you want the columns to be lined up. I'd suggest a perl script. doug Fornito, Alexander wrote: -b doesn't seem to work. The command is below, and the format of the output, are below. Is thi

RE: [Freesurfer] Autorecon re-processing

2005-09-19 Thread Fornito, Alexander
Sorry, I missed it - forgive my absent mindedness :( Onto a more valid problem (I hope!), I've had trouble segmenting the olfactory sulcus on some of my images. The wm wolume seems to segment well, but the orig and/or white surface doesn't follow this. Rather than enter the olfacoty sulcus, on

RE: [Freesurfer] anatomical stats

2005-09-19 Thread Fornito, Alexander
Yeah, that's what I meant. That's fine, just wanted to make sure I wasn't doing it wrong! -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 9/20/2005 5:22 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject:Re: [Fre

RE: [Freesurfer] Autorecon re-processing

2005-09-19 Thread Bruce Fischl
probably susceptibility problems. Try putting some control points in the wm, but there may not be enough g/w contrast to get good surfaces. On Tue, 20 Sep 2005, Fornito, Alexander wrote: Sorry, I missed it - forgive my absent mindedness :( Onto a more valid problem (I hope!), I've had tro