a3128u:/Applications FVila$ export FREESURFER_HOME=/Applications/freesurfer
a3128u:/Applications FVila$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME       /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Applications/freesurfer/subjects
MNI_DIR           /Applications/freesurfer/mni
FSL_DIR           /users/FVila/fsl
a3128u:/Applications FVila$ recon-all -i /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz -subjid FS_struct.nii.gz ERROR: You are trying to re-run an existing subject with (possibly)
 new input data (-i). If this is truly new input data, you should delete
 the subject folder and re-run, or specify a different subject name.
 If you are just continuing an analysis of an existing subject, then 
 omit all -i flags.
a3128u:/Applications FVila$ recon-all -i /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz -subjid FS_struct.nii.gz 
Subject Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0
Current Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
Darwin a3128u.bcricwh.lan 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc
tcsh: talairach_avi: Command not found.
tcsh: mri_watershed: Command not found.
tcsh: mri_segment: Command not found.
tcsh: mri_tessellate: Command not found.
tcsh: mri_concatenate_lta: Command not found.
tcsh: mri_normalize_tp2: Command not found.
tcsh: mris_smooth: Command not found.
tcsh: mris_inflate: Command not found.
tcsh: mris_curvature: Command not found.
tcsh: mris_sphere: Command not found.
tcsh: mris_fix_topology: Command not found.
tcsh: mris_topo_fixer: Command not found.
tcsh: mris_ca_label: Command not found.
tcsh: mris_euler_number: Command not found.
tcsh: mris_make_surfaces: Command not found.
tcsh: mris_register: Command not found.
tcsh: mris_volmask: Command not found.
tcsh: mris_anatomical_stats: Command not found.
tcsh: mrisp_paint: Command not found.
tcsh: mris_curvature_stats: Command not found.
tcsh: mris_calc: Command not found.
tcsh: mri_robust_register: Command not found.
tcsh: mri_robust_template: Command not found.
tcsh: mri_segstats: Command not found.
/Applications/freesurfer/subjects/FS_struct.nii.gz
\n mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz \n
mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz...

#------------------------------------------

recon-all -s FS_struct.nii.gz finished without error at Wed Jul 25 16:46:00 PDT 2012
done