from:"Remy Wahnoun"

[Freesurfer] recon-all ERROR, no idea why

2014-06-23 Thread Remy Wahnoun

hello, freesurfers,
Im having trouble using recon-all, I tried the prebuilt virtual machine and
a fresh unbuntu install without luck.
Would anyone have a look at my recon-all.log? I cant spot any error.
*Thanks *

*Rémy Wahnoun, PhD*
Biomedical Research Group Manager
Barrow Neurological Institute at Phoenix Children's Hospital
Adjunct Faculty, Arizona State University
*www.NeuralControl.net *






Mon Jun 23 11:35:42 EDT 2014
/media/sf_Imagery/FreeSurfer/xx
/usr/local/freesurfer/bin/recon-all
-i
/media/sf_Imagery/Sorted/xx/xx_S601_MRI_BRAIN_WO_CONTRAST_TRANSVERSAL(110)/ser601img1.dcm
-subjid xx -sd /media/sf_Imagery/FreeSurfer -all
subjid xx
setenv SUBJECTS_DIR /media/sf_Imagery/FreeSurfer
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0
Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48
UTC 2014 i686 i686 i386 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 64 kbytes
maxproc  28136
maxlocks unlimited
maxsignal28136
maxmessage   819200
maxnice  0
maxrtprio0
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:   3616064 6924002923664  0  94528 405020
-/+ buffers/cache: 1928523423212
Swap:  1944572  01944572


program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks 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: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May
13 2013 18:53:32  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter Exp $  User: fsuser  Machine: xubuntu-VirtualBox  Platform: Linux
 PlatformVersion: 3.2.0-64-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: 2014/06/23-15:35:42-GMT
 BuildTimeStamp: May 13 2013 18:53:32  CVS: $Id: tkregister2.c,v 1.121.2.1
2011/03/28 20:25:16 greve Exp $  User: fsuser  Machine: xubuntu-VirtualBox
 Platform: Linux  PlatformVersion: 3.2.0-64-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: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May
13 2013 18:53:32  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14
nicks Exp $  User: fsuser  Machine: xubuntu-VirtualBox  Platform: Linux
 PlatformVersion: 3.2.0-64-generic  CompilerName: GCC  CompilerVersion:
30400
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion:
$Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May
13 2013 18:53:32  CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32
nicks Exp $  User: fsuser  Machine: xubuntu-VirtualBox  Platform: Linux
 PlatformVersion: 3.2.0-64-generic  CompilerName: GCC  CompilerVersion:
30400
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion:
$Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May
13 2013 18:53:32  CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08
22:18:44 nicks Exp $  User: fsuser  Machine: xubuntu-VirtualBox  Platform:
Linux  PlatformVersion: 3.2.0-64-generic  CompilerName: GCC
 CompilerVersion: 30400
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name:
stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May 13 2013
18:53:32  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $
 User: fsuser  Machine: xubuntu-VirtualBox  Platform: Linux
 PlatformVersion: 3.2.0-64-generic  CompilerName: GCC  CompilerVersion:
30400
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion:
$Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May
13 2013 18:53:32  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks
Exp $  User: fsuser  Machine: xubuntu-VirtualBox  Platform: Linux
 PlatformVersion: 3.2.0-64-generic  CompilerName: GCC  CompilerVersion:
30400
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion:
$Name: stable5 $  TimeStamp: 2014/06/23-15:35:42-GMT  BuildTimeStamp: May
13 2013 18:53:32  CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02
16:26:15 greve Exp $  User: fsuser  Machine: xubuntu-VirtualBox  Platform:
Linux  PlatformVersion: 3.2.0-64-generic  CompilerName: GCC
 CompilerVersion: 30400
ProgramName: mri_em_register  Pr

Re: [Freesurfer] recon-all ERROR, no idea why

2014-06-23 Thread Remy Wahnoun

Thanks Douglas,

I definitely appreciate your help.

Here is what it Spit out,



*Rémy Wahnoun, PhD*

Biomedical Research Group Manager

Barrow Neurological Institute at Phoenix Children's Hospital

Adjunct Faculty, Arizona State University

*www.NeuralControl.net *





set echo = 1 ;

set debug = 1 ;

set debug = 1

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 11 != 0 )



set flag = $argv[1] ; shift ;

set flag = --n

shift



switch ( $flag )

switch ( --n )

if ( $#argv == 0 ) goto arg1err ;

if ( 10 == 0 ) goto arg1err

set nIters = $argv[1] ; shift ;

set nIters = 1

shift

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 9 != 0 )



set flag = $argv[1] ; shift ;

set flag = --proto-iters

shift



switch ( $flag )

switch ( --proto-iters )

if ( $#argv == 0 ) goto arg1err ;

if ( 8 == 0 ) goto arg1err

set nProtoIters = $argv[1] ; shift ;

set nProtoIters = 1000

shift

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 7 != 0 )



set flag = $argv[1] ; shift ;

set flag = --distance

shift



switch ( $flag )

switch ( --distance )

if ( $#argv == 0 ) goto arg1err ;

if ( 6 == 0 ) goto arg1err

set Distance = $argv[1] ; shift ;

set Distance = 50

shift

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 5 != 0 )



set flag = $argv[1] ; shift ;

set flag = --no-rescale

shift



switch ( $flag )

switch ( --no-rescale )

set DoRescale = 0 ;

set DoRescale = 0

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 4 != 0 )



set flag = $argv[1] ; shift ;

set flag = --i

shift



switch ( $flag )

switch ( --i )

if ( $#argv == 0 ) goto arg1err ;

if ( 3 == 0 ) goto arg1err

set InVol = $argv[1] ; shift ;

set InVol = orig.mgz

shift

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 2 != 0 )



set flag = $argv[1] ; shift ;

set flag = --o

shift



switch ( $flag )

switch ( --o )

if ( $#argv == 0 ) goto arg1err ;

if ( 1 == 0 ) goto arg1err

set OutVol = $argv[1] ; shift ;

set OutVol = orig_nu.mgz

shift

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 0 != 0 )



goto parse_args_return ;

goto parse_args_return





goto check_params ;

goto check_params

if ( $#InVol == 0 ) then

if ( 1 == 0 ) then

if ( ! -e $InVol ) then

if ( ! -e orig.mgz ) then

if ( $#OutVol == 0 ) then

if ( 1 == 0 ) then



goto check_params_return ;

goto check_params_return



set OutDir = `dirname $OutVol` ;

set OutDir = `dirname $OutVol`

dirname orig_nu.mgz

mkdir -p $OutDir ;

mkdir -p .



if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log

if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log

set LF = ./mri_nu_correct.mni.log

if ( -e $LF ) mv $LF $LF.bak

if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log
./mri_nu_correct.mni.log.bak

mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak



pwd | tee -a $LF

pwd

tee -a ./mri_nu_correct.mni.log

/media/sf_Imagery/FreeSurfer/xx/mri

which mri_nu_correct.mni | tee -a $LF

which mri_nu_correct.mni

tee -a ./mri_nu_correct.mni.log

/usr/local/freesurfer/bin/mri_nu_correct.mni

echo $cmdargs | tee -a $LF

echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz

tee -a ./mri_nu_correct.mni.log

--debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz
--o orig_nu.mgz

echo "nIters $nIters" | tee -a $LF

echo nIters 1

tee -a ./mri_nu_correct.mni.log

nIters 1

echo $VERSION | tee -a $LF

tee -a ./mri_nu_correct.mni.log

echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $

$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $

uname -a | tee -a $LF

uname -a

tee -a ./mri_nu_correct.mni.log

Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48
UTC 2014 i686 i686 i386 GNU/Linux

date | tee -a $LF

date

tee -a ./mri_nu_correct.mni.log

Mon Jun 23 15:32:45 EDT 2014

nu_correct -version | tee -a $LF

nu_correct -version

tee -a ./mri_nu_correct.mni.log

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



if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$

if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745

set tmpdir = ./tmp.mri_nu_correct.mni.1745

mkdir -p $tmpdir

mkdir -p ./tmp.mri_nu_correct.mni.1745

echo "tmpdir is $tmpdir" | tee -a $LF

echo tmpdir is ./tmp.mri_nu_correct.mni.1745

tee -a ./mri_nu_correct.mni.log

tmpdir is ./tmp.mri_nu_correct.mni.1745





set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc )

set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc )

if ( $UseFloat ) set cmd = ( $cmd -odt float )

if ( 1 ) set cmd = ( mri_convert orig.mgz
./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float )

set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt
float )

pwd | & tee -a $LF

pwd

tee -a ./mri_nu_correct.mni.log

/media/sf_Imagery/FreeSurfer/xx/mri

echo $cmd | & tee -a

Re: [Freesurfer] recon-all ERROR, no idea why

2014-06-30 Thread Remy Wahnoun

Thanks Douglas,
orig.mgz looks fine to me. Do you know if there is any detailed log i could
look into? Or maybe process tasks one after the other?


*Rémy Wahnoun, PhD*
Biomedical Research Group Manager
Barrow Neurological Institute at Phoenix Children's Hospital
Adjunct Faculty, Arizona State University
*www.NeuralControl.net <http://www.NeuralControl.net>*


On Wed, Jun 25, 2014 at 7:40 AM, Douglas N Greve 
wrote:

>
> This is dying somewhere in the MNI nu_correct code. Look at the orig.mgz
> to see if that looks ok
>
>
> On 06/23/2014 03:58 PM, Remy Wahnoun wrote:
> >
> > Thanks Douglas,
> >
> > I definitely appreciate your help.
> >
> > Here is what it Spit out,
> >
> > *Rémy Wahnoun, PhD*
> >
> > Biomedical Research Group Manager
> >
> > Barrow Neurological Institute at Phoenix Children's Hospital
> >
> > Adjunct Faculty, Arizona State University
> >
> > /www.NeuralControl.net <http://www.neuralcontrol.net/>/
> >
> > set echo = 1 ;
> >
> > set debug = 1 ;
> >
> > set debug = 1
> >
> > breaksw
> >
> > breaksw
> >
> > end
> >
> > end
> >
> > while ( $#argv != 0 )
> >
> > while ( 11 != 0 )
> >
> > set flag = $argv[1] ; shift ;
> >
> > set flag = --n
> >
> > shift
> >
> > switch ( $flag )
> >
> > switch ( --n )
> >
> > if ( $#argv == 0 ) goto arg1err ;
> >
> > if ( 10 == 0 ) goto arg1err
> >
> > set nIters = $argv[1] ; shift ;
> >
> > set nIters = 1
> >
> > shift
> >
> > breaksw
> >
> > breaksw
> >
> > end
> >
> > end
> >
> > while ( $#argv != 0 )
> >
> > while ( 9 != 0 )
> >
> > set flag = $argv[1] ; shift ;
> >
> > set flag = --proto-iters
> >
> > shift
> >
> > switch ( $flag )
> >
> > switch ( --proto-iters )
> >
> > if ( $#argv == 0 ) goto arg1err ;
> >
> > if ( 8 == 0 ) goto arg1err
> >
> > set nProtoIters = $argv[1] ; shift ;
> >
> > set nProtoIters = 1000
> >
> > shift
> >
> > breaksw
> >
> > breaksw
> >
> > end
> >
> > end
> >
> > while ( $#argv != 0 )
> >
> > while ( 7 != 0 )
> >
> > set flag = $argv[1] ; shift ;
> >
> > set flag = --distance
> >
> > shift
> >
> > switch ( $flag )
> >
> > switch ( --distance )
> >
> > if ( $#argv == 0 ) goto arg1err ;
> >
> > if ( 6 == 0 ) goto arg1err
> >
> > set Distance = $argv[1] ; shift ;
> >
> > set Distance = 50
> >
> > shift
> >
> > breaksw
> >
> > breaksw
> >
> > end
> >
> > end
> >
> > while ( $#argv != 0 )
> >
> > while ( 5 != 0 )
> >
> > set flag = $argv[1] ; shift ;
> >
> > set flag = --no-rescale
> >
> > shift
> >
> > switch ( $flag )
> >
> > switch ( --no-rescale )
> >
> > set DoRescale = 0 ;
> >
> > set DoRescale = 0
> >
> > breaksw
> >
> > breaksw
> >
> > end
> >
> > end
> >
> > while ( $#argv != 0 )
> >
> > while ( 4 != 0 )
> >
> > set flag = $argv[1] ; shift ;
> >
> > set flag = --i
> >
> > shift
> >
> > switch ( $flag )
> >
> > switch ( --i )
> >
> > if ( $#argv == 0 ) goto arg1err ;
> >
> > if ( 3 == 0 ) goto arg1err
> >
> > set InVol = $argv[1] ; shift ;
> >
> > set InVol = orig.mgz
> >
> > shift
> >
> > breaksw
> >
> > breaksw
> >
> > end
> >
> > end
> >
> > while ( $#argv != 0 )
> >
> > while ( 2 != 0 )
> >
> > set flag = $argv[1] ; shift ;
> >
> > set flag = --o
> >
> > shift
> >
> > switch ( $flag )
> >
> > switch ( --o )
> >
> > if ( $#argv == 0 ) goto arg1err ;
> >
> > if ( 1 == 0 ) goto arg1err
> >
> > set OutVol = $argv[1] ; shift ;
> >
> > set OutVol = orig_nu.mgz
> >
> > shift
> >
> > breaksw
> >
> > breaksw
> >
> > end
> >
> > end
> >
> > while ( $#argv != 0 )
> >
> > while ( 0 != 0 )
> >
> > goto parse_args_return ;
> >
> > goto parse_args_return
> >
> > goto check_params ;
> >
> > goto check_params
> >
> > if ( $#InVol == 0 ) then
>

[Freesurfer] recon-all ERROR, no idea why

Re: [Freesurfer] recon-all ERROR, no idea why

Re: [Freesurfer] recon-all ERROR, no idea why

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