hi folks - I'm trying to get freesurfer (the latest Tiger snapshot) working on my mac but I'm having a problem with recon-all. If I try to apply it to the bert data included in the distribution, it seems to set up ok but then it doesn't actually do anything. here is the output from "recon-all-nmr -all -subjid bert" (same thing happens if I just use recon-all):
Fri Jul 22 13:33:27 PDT 2005
/Users/Shared/freesurfer/bin//recon-all-nmr
-all -subjid bert
/Users/Shared/freesurfer/subjects/bert
subjid bert
SUBJECTS_DIR /Users/Shared/freesurfer/subjects
FREESURFER_HOME /Users/Shared/freesurfer
AutoSeg Enable = 1
Darwin
########################################
program versions used
$Id: recon-all-nmr,v 1.71 2005/07/11 22:46:53 greve Exp $
$Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $
mri_convert --version
$
$Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 b
ert Exp $
minctracc.c
$Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11 2004/
02/12 05:54:22 rotor Exp $
!p$Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19
:02:51 bert Exp $
$Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:4
9 bert Exp $
$Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $
mri_convert --version
$
# $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $
# $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $
$
$
$
$
$
$
$
$
$
$
$
$
$
$
$
$
$
$
$
$
#######################################
Using COR format
here it just stops, which is presumably not the expected behavior with the -all flag. I also tried with a new dataset converted to mgz format and with the -autorecon1 option and the same thing happens. Any ideas what might be going on here?
cheers
russ
---
Russell A. Poldrack, Ph.d.
Assistant Professor
UCLA Department of Psychology
Franz Hall, Box 951563
Los Angeles, CA 90095-1563
phone: 310-794-1224
fax: 310-206-5895
email: poldrack@ucla.edu
web: www.poldracklab.org