Hallo, now I use cc...
Actually I gave you wrong info - I DID rename file patient.mgz to 001.mgz
and not orig.mgz as I wrote before, sorry.
I attach recon-all.log file with errors from my last run. It is about nu_
correct.
Thanks for help, Petr
---------- Původní zpráva ----------
Od: Louis Nicholas Vinke <vi...@nmr.mgh.harvard.edu>
Datum: 17. 1. 2013
Předmět: Re: [Freesurfer] nu_correct problem (fwd)
"Hi Petr,
Try renaming /subject/patient/mri/orig/orig.mgz to
/subject/patient/mri/orig/001.mgz and rerunning recon-all. The orig.mgz
file is created later on in the recon-all stream.
-Louis
On Thu, 17 Jan 2013, Louis Nicholas Vinke wrote:
> Please remember to cc the list.
>
> ---------- Forwarded message ----------
> Date: Thu, 17 Jan 2013 11:07:43 +0100 (CET)
> From: zach.p...@post.cz
> To: Louis Nicholas Vinke <vi...@nmr.mgh.harvard.edu>
> Subject: Re: Re: [Freesurfer] nu_correct problem
>
>
> Hallo, I use VB Ubuntu on standard PC machine downloaded from Freesurfer
web
> page
>
> (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi,
Documentation)
>
>
>
> I´ll send recon-all.log file later on I have it on another PC.
>
>
>
> Orig.mgz file - thats also problem. What I did: when running recon-all
> -subjid name -autorecon1 I get
> error: no /mri/orig/orig.mgz file. I looked into patients /mri directory
> and this path and file is
> not there. So that I created directory /orig in /mri and copied there
> converted patient.mgz file there
> and renamed it to orig.mgz. So that I have
> /subject/patient/mri/orig/orig.mgz. Maybe thats what is
> wrong? How do you get normally orig.mgz file?
>
>
>
> Thanks, Petr
>
>
>
>
>
>
> ---------- Původní zpráva ----------
> Od: Louis Nicholas Vinke <vi...@nmr.mgh.harvard.edu>
> Datum: 16. 1. 2013
> Předmět: Re: [Freesurfer] nu_correct problem
>
>
> Hi Petr,
> Can you provide us with some more details? Which version of FreeSurfer
> are you using and on what platform? Could you attach a copy of the
> recon-all.log file for one of these cases so we can read the full error
> reported?
>
> Have you tried looking at the orig.mgz which is generated prior to the
> mri_nu_correct.mni step to see if it looks reasonable?
> -Louis
>
> On Wed, 16 Jan 2013, zach.p...@post.cz wrote:
>
> >
> >
> > Dear members,
> >
> > when I run recon_all -subjid name -autorecon1 process stops with
> ERROR at nu_correct. This
> happens for
> > DICOM but also IMA file type. I tried several brains. Do you have any
> idea what is wrong?
> >
> > Thanks much, Petr Zach
> >
> >
> >
>
>
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>"
Thu Jan 17 14:40:30 EST 2013
/home/virtualuser/freesurfer/subjects/s
/home/virtualuser/freesurfer/bin/recon-all
-subjid s -autorecon1
subjid s
setenv SUBJECTS_DIR /home/virtualuser/freesurfer/subjects
FREESURFER_HOME /home/virtualuser/freesurfer
Actual FREESURFER_HOME /home/virtualuser/freesurfer
build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.1.0
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc unlimited
total used free shared buffers cached
Mem: 458880 306100 152780 0 31844 134440
-/+ buffers/cache: 139816 319064
Swap: 530104 0 530104
########################################
program versions used
$Id: recon-all,v 1.395 2011/05/18 23:01:39 krish Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:31-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:32-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
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
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:32-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:33-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:33-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:33-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:34-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:34-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_label2label.c,v 1.40 2011/03/02 00:04:22 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:35-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:35-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:36-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:36-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:36-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:37-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:37-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:38-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:38-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:38-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:39-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:39-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:40-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:40-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:41-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:41-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:41-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:42-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:42-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:43-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:43-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:44-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:44-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:44-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:45-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:46-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:46-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:46-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:47-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:47-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
#######################################
GCADIR /home/virtualuser/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /home/virtualuser/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
#--------------------------------------------
#@# MotionCor Thu Jan 17 14:40:48 EST 2013
ERROR: no run data found in /home/virtualuser/freesurfer/subjects/s/mri. Make sure to
have a volume called 001.mgz in /home/virtualuser/freesurfer/subjects/s/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
recon-all -s s exited with ERRORS at Thu Jan 17 14:40:48 EST 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
New invocation of recon-all
Thu Jan 17 14:42:08 EST 2013
/home/virtualuser/freesurfer/subjects/s
/home/virtualuser/freesurfer/bin/recon-all
-subjid s -autorecon1
subjid s
setenv SUBJECTS_DIR /home/virtualuser/freesurfer/subjects
FREESURFER_HOME /home/virtualuser/freesurfer
Actual FREESURFER_HOME /home/virtualuser/freesurfer
build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.1.0
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc unlimited
total used free shared buffers cached
Mem: 458880 421520 37360 0 32176 246764
-/+ buffers/cache: 142580 316300
Swap: 530104 0 530104
########################################
program versions used
$Id: recon-all,v 1.395 2011/05/18 23:01:39 krish Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:08-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:09-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
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
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:09-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:09-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:09-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:09-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:10-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:10-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_label2label.c,v 1.40 2011/03/02 00:04:22 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:10-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:10-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:10-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:10-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:11-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:11-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:11-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:11-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:11-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:11-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:12-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:12-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:12-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:12-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:12-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:13-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:13-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:13-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:13-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:13-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:14-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:14-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:14-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:14-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:14-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:15-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:15-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:15-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:15-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:42:15-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400
#######################################
GCADIR /home/virtualuser/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /home/virtualuser/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
#--------------------------------------------
#@# MotionCor Thu Jan 17 14:42:16 EST 2013
Found 1 runs
/home/virtualuser/freesurfer/subjects/s/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/virtualuser/freesurfer/subjects/s/mri/orig/001.mgz /home/virtualuser/freesurfer/subjects/s/mri/rawavg.mgz
/home/virtualuser/freesurfer/subjects/s
mri_convert /home/virtualuser/freesurfer/subjects/s/mri/rawavg.mgz /home/virtualuser/freesurfer/subjects/s/mri/orig.mgz --conform
mri_convert /home/virtualuser/freesurfer/subjects/s/mri/rawavg.mgz /home/virtualuser/freesurfer/subjects/s/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from /home/virtualuser/freesurfer/subjects/s/mri/rawavg.mgz...
TR=11.40, TE=4.40, TI=20.00, flip angle=10.00
i_ras = (-0, -1, -0)
j_ras = (-0.0348995, 0, -0.999391)
k_ras = (-0.999391, -0, 0.0349)
Original Data has (1, 1, 1) mm size and (256, 256, 160) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /home/virtualuser/freesurfer/subjects/s/mri/orig.mgz...
mri_add_xform_to_header -c /home/virtualuser/freesurfer/subjects/s/mri/transforms/talairach.xfm /home/virtualuser/freesurfer/subjects/s/mri/orig.mgz /home/virtualuser/freesurfer/subjects/s/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu Jan 17 14:42:50 EST 2013
/home/virtualuser/freesurfer/subjects/s/mri
talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Thu Jan 17 14:45:16 EST 2013
/home/virtualuser/freesurfer/subjects/s/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6301, pval=0.3663 >= threshold=0.0050)
awk -f /home/virtualuser/freesurfer/bin/extract_talairach_avi_QA.awk /home/virtualuser/freesurfer/subjects/s/mri/transforms/talairach_avi.log
TalAviQA: 0.97931
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Thu Jan 17 14:45:17 EST 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/home/virtualuser/freesurfer/subjects/s/mri
/home/virtualuser/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 2011/03/02 20:16:39 nicks Exp $
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
Thu Jan 17 14:45:18 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.4215
/home/virtualuser/freesurfer/subjects/s/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4215/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4215/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from orig.mgz...
TR=11.40, TE=4.40, TI=20.00, flip angle=10.00
i_ras = (-1, 0, -3.72529e-08)
j_ras = (3.72529e-08, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.4215/nu0.mnc...
Outputting Volume: ............................................................
--------------------------------------------------------
Iteration 1 Thu Jan 17 14:45:39 EST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.4215/nu0.mnc ./tmp.mri_nu_correct.mni.4215/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4215/0/
[virtualuser@FreeSurfer:/home/virtualuser/freesurfer/subjects/s/mri/] [2013-01-17 14:45:40] running:
/home/virtualuser/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4215/0/ ./tmp.mri_nu_correct.mni.4215/nu0.mnc ./tmp.mri_nu_correct.mni.4215/nu1.imp
Assertion failed at line 827 in file templates/CachedArray.cc
nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)
ERROR: nu_correct
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
recon-all -s s exited with ERRORS at Thu Jan 17 14:45:45 EST 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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