[Freesurfer] problem on freesurfer

2010-03-04 Thread Xiaoying Tang
Hi Nick, Sorry, I am not sure whether I can successfully post my problem on the mailing list. So I send you the email and cc it to the mailing list. I now have a problem on freesurfer. After run auto-recon2, I am supposed to get grey matter and white matter. The white matter is in the form of w

Re: [Freesurfer] the input file of recon-all

2010-03-04 Thread liyuanyuan60
Too much thanks for your reply! I will try the 4.5.0 version Best wishes! 2010-03-05 liyuanyuan60 发件人: Nick Schmansky 发送时间: 2010-03-04 22:00:21 收件人: liyuanyuan60 抄送: Freesurfer 主题: Re: [Freesurfer] the input file of recon-all v4.3.0 has some randomness in its algorithms which accou

Re: [Freesurfer] mri_watershed and mri_make_bem_surfaces

2010-03-04 Thread Bruce Fischl
Hi Andres, those errors are probably not related (tkmedit tries to read an array of cortical surfaces that don't exist for the BEM analysis). I'm not sure what BEM mesh editing tools exist - maybe Matti knows? cheers, Bruce On Wed, 3 Mar 2010, Andres Felipe Salazar Gomez wrote: Hello Fre

Re: [Freesurfer] merging rh and lh surfaces

2010-03-04 Thread Raghav Puranmalka
Hi all - I was trying to merge rh and lh surfaces. I succeeded after reading the mailing list archives from March 2009 found at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09665.html. I following this guide: you can get something like what you want with cd $SUBJECTS_DIR/subj

Re: [Freesurfer] Cerebellum volume analysis

2010-03-04 Thread Bruce Fischl
Hi Cindy, this is on our to-do list. Maybe David can give you an update as to where we are? cheers, Bruce On Thu, 4 Mar 2010, Cindy Eckart wrote: Dear FreeSurfers, I plan to do a cerebellar volume analysis in a rather large clinical sample and thereto originally aimed to follow the instr

[Freesurfer] Cerebellum volume analysis

2010-03-04 Thread Cindy Eckart
Dear FreeSurfers, I plan to do a cerebellar volume analysis in a rather large clinical sample and thereto originally aimed to follow the instructions of Makris and colleaugues (2003, 2005). Unfortunatly I was not able to get access to all the necessary software and accordingly I am forced to im

Re: [Freesurfer] the input file of recon-all

2010-03-04 Thread Nick Schmansky
v4.3.0 has some randomness in its algorithms which account for these differences. if you want the results to repeat from run to run, add the -norandomness flag, or use v4.5.0. n. On Wed, 2010-03-03 at 23:27 +0800, liyuanyuan60 wrote: > > HI Bruce and freesurfers > I have a question about the i