General info:
fsuser@xubuntu-VirtualBox:~/share/SMIP_MNI_structural_files/b_s_20131018_124417$ which freesurfer
/usr/local/freesurfer/bin/freesurfer
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Debian version: wheezy/sid
Kernel info: Linux 3.2.0-56-generic i686
Unsuccessful Run:
xubuntu-VirtualBox:~/share/SMIP_MNI_structural_files/boucher_suzanne_20131018_12 4417> recon-all -subjid b_s_20131018_fs -all
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 UTC 2013 i686 i686 i386 GNU/Linux
#--------------------------------------------
#@# MotionCor Fri Nov 15 16:30:12 EST 2013
Found 1 runs
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
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/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig/001.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs
mri_convert /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz --conform
mri_convert /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.0156845, -0.970744, 0.239606)
j_ras = (0.0185749, 0.239877, 0.970626)
k_ras = (0.999704, 0.0107731, -0.0217938)
Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz...
mri_add_xform_to_header -c /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/transforms/talairach.xfm /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Fri Nov 15 16:30:45 EST 2013
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 UTC 2013 i686 i686 i386 GNU/Linux
recon-all -s b_s_20131018_fs exited with ERRORS at Fri Nov 15 16:30:58 EST 2013
SUCCESSFUL RUN:
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Fri Nov 15 15:53:35 EST 2013
/usr/local/freesurfer/subjects/bert/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
INFO: transforms/talairach.xfm already exists!
The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm
This is done to retain any edits made to transforms/talairach.xfm
Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Fri Nov 15 15:55:03 EST 2013
/usr/local/freesurfer/subjects/bert/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7614, pval=0.6675 >= threshold=0.0050)
awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/bert/mri/transforms/talairach_avi.log
tal_QC_AZS /usr/local/freesurfer/subjects/bert/mri/transforms/talairach_avi.log
TalAviQA: 0.97409
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Fri Nov 15 15:55:03 EST 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/usr/local/freesurfer/subjects/bert/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 UTC 2013 i686 i686 i386 GNU/Linux
Fri Nov 15 15:55:03 EST 2013
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13
tmpdir is ./tmp.mri_nu_correct.mni.10351
/usr/local/freesurfer/subjects/bert/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10351/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10351/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=0.00, 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)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.10351/nu0.mnc...