Re: [Freesurfer] Average Brain atlas

2005-07-27 Thread Bruce Fischl
various uninteresting things. We'll be distributing two new atlases soon - one for mp-rage and one for FLASH. cheers, Bruce On Wed, 27 Jul 2005, Tracy Wang wrote: Hi all, I was just wondering what the difference is between the talairach_mixed.gca, talairach_mixed_a1_new_b.gca and talairach_

[Freesurfer] Average Brain atlas

2005-07-27 Thread Tracy Wang
Hi all, I was just wondering what the difference is between the talairach_mixed.gca, talairach_mixed_a1_new_b.gca and talairach_mixed_new_b.gca Thanks! Tracy Wang Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO

Re: [Freesurfer] Freesurfer OS problems

2005-07-27 Thread Nick Schmansky
Hans, Hello, from your comments, I think I spoke too soon in stating that your installation completed successfully. In a successful installation, the freesurfer/bin directory is placed in the path. Also, the MINC tools, which are included in the Mac OS X Tiger 'full' distribution, are installed

Re: [Freesurfer] Perl problems with mac install

2005-07-27 Thread Nick Schmansky
Russ, Thank you for pointing this out. Our script does indeed need an update to account for a pre-defined PERL5LIB (ie appending to it). This will appear in the upcoming release. Nick On Wed, 2005-07-27 at 09:58 -0700, Russ Poldrack wrote: > hi - yes, nu_correct complained that it couldn't fin

Re: [Freesurfer] Freesurfer OS problems

2005-07-27 Thread Hans Johnson
Nick, It does seem that the freesurfer files are installed on my Mac. Just some minor notes: 1) Bash/POSIX shell is not supported. 'source /Users/Shared/freesurfer/SetUpFreeSurfer.csh' 2) After changing to tcsh and resourcing 'source /Users/Shared/freesurfer/SetUpFreeSurfer.csh' the PATH does no

Re: [Freesurfer] mris_smooth

2005-07-27 Thread Bruce Fischl
hmmm, never saw that before. If you can put the data somewhere we can get to it, we'll take a look. Bruce On Wed, 27 Jul 2005, Antao Du wrote: Hi, When I run recon-all stage2, I got the following error message but I can't get the answer from the email list. Can anyone help me what is wrong?

[Freesurfer] mris_smooth

2005-07-27 Thread Antao Du
Hi, When I run recon-all stage2, I got the following error message but I can't get the answer from the email list. Can anyone help me what is wrong? thanks, Antao - Starting Hemisphere rh - Tessellate rh Wed Jul 27 10:23:11 PDT 2005 mri_t

Re: [Freesurfer] Perl problems with mac install

2005-07-27 Thread Russ Poldrack
hi - yes, nu_correct complained that it couldn't find various Perl files.  I did source the FreeSurferEnv.csh file before running - it seems that the PERL5LIB environment variable is not getting properly set by the script, as this is what I see even after sourcing the script:[russ-poldracks-power-m

Re: [Freesurfer] Freesurfer OS problems

2005-07-27 Thread Hans Johnson
Bruce, Thanks for the reply. Yes we have a version of FreeSurfer running (Feb. 2004 + misc. patches that you provided through June 2004). The problem is that our working version FreeSurfer is only running on RedHat 9. We have one machine that we have not been allowed to upgrade because of this.

Re: [Freesurfer] Freesurfer OS problems

2005-07-27 Thread Nick Schmansky
Hans, Hello, Does your Mac OS X Tiger freesurfer installation work despite the reported error? I suspect that the problem is that it failed to write the 'receipt' to the /Library/Receipt directory, which requires Administrator privileges. This is the only part of the install (as currently impl

[Freesurfer] Freesurfer OS problems

2005-07-27 Thread Hans Johnson
Hello Freesurfer Developers, We are attempting to install freesurfer as one of our standard image processing packages at the Mental Health Clinical Research Center Image Processing Lab at The University of Iowa. Our environment consists of Redhat EL3WS, Redhat EL4WS, and MacOSX 10.4 operating sys