[iwobohr@huxley FMRI]$ recon-all -autorecon1 -i NCVI-JR001TH_T1WIR_brain-conv.nii.gz
  -subjid test -all -force
INFO: /home/iwobohr/subjects/test exists with -i, but -force specified.
Deleting any previous source volumes
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0
INFO: SUBJECTS_DIR is /home/iwobohr/subjects
Actual FREESURFER_HOME /opt/freesurfer
-rw-rw-r-- 1 iwobohr iwobohr 99469 May 28 16:36 /home/iwobohr/subjects/test/scripts/
recon-all.log
Linux huxley 2.6.18-128.1.1.el5 #1 SMP Tue Feb 10 11:36:29 EST 2009 x86_64 x86_64 x8
6_64 GNU/Linux
nu_correct: Command not found.
/home/iwobohr/subjects/test

 mri_convert /home/iwobohr/FMRI/NCVI-JR001TH_T1WIR_brain-conv.nii.gz /home/iwobohr/s
ubjects/test/mri/orig/001.mgz

mri_convert /home/iwobohr/FMRI/NCVI-JR001TH_T1WIR_brain-conv.nii.gz /home/iwobohr/su
bjects/test/mri/orig/001.mgz
$Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $
reading from /home/iwobohr/FMRI/NCVI-JR001TH_T1WIR_brain-conv.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 /home/iwobohr/subjects/test/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Fri May 29 10:47:30 BST 2009
Found 1 runs
/home/iwobohr/subjects/test/mri/orig/001.mgz
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /home/iwobohr/subjects/test/mri/orig/001.mgz /home/iwobohr/subjects/test/mri/raw            avg.mgz

/home/iwobohr/subjects/test

 mri_convert /home/iwobohr/subjects/test/mri/rawavg.mgz /home/iwobohr/subjects/test/            mri/orig.mgz --conform

mri_convert /home/iwobohr/subjects/test/mri/rawavg.mgz /home/iwobohr/subjects/test/m            ri/orig.mgz --conform
$Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $
reading from /home/iwobohr/subjects/test/mri/rawavg.mgz...
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)
Original Data has (0.938, 0.9, 0.938) mm size and (256, 180, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from 3 to 0 (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /home/iwobohr/subjects/test/mri/orig.mgz...

 mri_add_xform_to_header -c /home/iwobohr/subjects/test/mri/transforms/talairach.xfm /home/iwobohr/subjects/test/mri/orig.mgz /home/iwobohr/subjects/test/mri/orig.mgz

INFO: extension is mgz
#--------------------------------------------
#@# Nu Intensity Correction Fri May 29 10:47:48 BST 2009

 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2

/home/iwobohr/subjects/test/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.7.2.1 2008/07/09 21:05:39 nicks Exp $
Linux huxley 2.6.18-128.1.1.el5 #1 SMP Tue Feb 10 11:36:29 EST 2009 x86_64 x86_64 x86_64 GNU/Linux
Fri May 29 10:47:48 BST 2009
nu_correct: Command not found.
tmpdir is ./tmp.mri_nu_correct.mni.30677
/home/iwobohr/subjects/test/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30677/nu0.mnc
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30677/nu0.mnc
$Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $
reading from orig.mgz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to ./tmp.mri_nu_correct.mni.30677/nu0.mnc...

--------------------------------------------------------
Iteration 1 Fri May 29 10:47:54 BST 2009
nu_correct -clobber ./tmp.mri_nu_correct.mni.30677/nu0.mnc ./tmp.mri_nu_correct.mni.30677/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30677/0/
nu_correct: Command not found.
ERROR: nu_correct