Hi Russ,
not sure what's going on with that. We'd made a bunch of changes over the last couple of weeks, so I'm attaching the most recent version. Also note that the most recent version assumes that you want to do subcortical segmetation, the atlas for which has not been released yet (a couple more weeks). To prevent subcort seg, run with -all -nosubcortseg.
doug
On Sat, 23 Jul 2005, Russ Poldrack wrote:
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