Re: [Freesurfer] thickness and curvature

I looked at the code and found another option for mris_thickness: -N for neighborhood size. For mris_make_surfaces, the default is 20, but for mris_thickness, the default is 2. So setting it to 20 gave the correct result. From: "Don Hagler" <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] CC: freesu

[Freesurfer] starting problems

Hello all, After sucessful installation, i am trying to run FREESURFER. The conversion to 001.mgz seems to work, but when i want to run recon- all i get the following output: recon-all -001 ERROR: Flag -001 unrecognized. -001 Linux localhost.localdomain 2.6.9-55.ELsmp #1 SMP Wed May 2 14:04:42 ED

Re: [Freesurfer] starting problems

Hi Thomas, try: recon-all --i --all --s --sd On Mon, 17 Sep 2007, Thomas Doring wrote: Hello all, After sucessful installation, i am trying to run FREESURFER. The conversion to 001.mgz seems to work, but when i want to run recon- all i get the following output: recon-all -001 ERROR: F

Re: [Freesurfer] qdoc BadMatch error

Lisa, Unfortunately, this is a problem that I have not been able to recreate locally with the operating systems I have available. It seems to occur just on Ubuntu. Have you tried updating the video driver? That is the only thing I can think to try. I will try to google-search this problem

RE: [Freesurfer] thickness and curvature

While we don't have access to de source code it would be interesting that most of the "tunning" keys are documented. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Don Hagler Sent: segunda-feira, 17 de setembro de 2007 04:01 To: [EMAIL PROTECTED] Cc: free

RE: [Freesurfer] thickness and curvature

we're trying :). And we will have a source release by the end of the year I think On Mon, 17 Sep 2007, Pedro Paulo Oliveira Jr wrote: While we don't have access to de source code it would be interesting that most of the "tunning" keys are documented. -Original Message- From: [EMAIL PRO

[Freesurfer] centos4_x86_64_V4.0 vs. centos4_V4.0

Hi all, I had tried to play with FreeSurfer centos4_x86_64_v4.0 on my laptop in the past two days, and found that the tksurfer did not show the brain surface correctly. Today, I installed the centos4_v4.0 on the same laptop. This version seems to work well. The only difference I have noticed by

Re: [Freesurfer] centos4_x86_64_V4.0 vs. centos4_V4.0

Xiangchuan Chen, The centos4_x86_64_v4.0 version of freesurfer should not use the shared lib version of libglut, but rather the static version, as the centos4_v4.0 version does. This is a mistake that will be fixed in the v4.0.1 release, later this week. Thanks for pointing this out. As for tkm

Re: Re: [Freesurfer] centos4_x86_64_V4.0 vs. centos4_V4.0

Hi Nick, Thank you for replying to my questions. I am glad to know why the centos4_x86_64_v4.0 version did not work on my laptop. For the tkmedit issue, the + and - icons next to the slice number entry box, and the arrow keys all work very well when I want to change the slice number one by one.

[Freesurfer] re-run FreeSurfer with v4

Hi all, I am working on 80 subjects' data with the following work flow: 1. -autorecon1 2. edit talairach registration 3. -autorecon1 4. -autorecon2 5. edit brainmask.mgz 6. edit wm.mgz 7. -autorecon2-wm 8. -autorecon3 I have already finished this work flow for 30 subjects with FreeSurfer v3.05.

Re: [Freesurfer] re-run FreeSurfer with v4

Hi Xiangchuan Avi Snyder's new talairach doesn't seem to fail anymore, and the skullstrip failures are now extremely rate, so you might just let the whole thing chug through and only check it at the end to make sure the surfaces are accurate. cheers, Bruce On Mon, 17 Sep 2007, Xiangchuan Ch