On Fri, May 24, 2013 at 4:28 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:

Not quite... What is the ouput when you type "ls -l libreadline*" in the /lib64 directory?

On 05/24/2013 04:23 PM, Erin W. E. Dickie wrote:

Yes I see it in /lib64. So I just need to add /lib64 to the PATH and it
should work?
Thanks,
Erin

On Fri, May 24, 2013 at 4:18 PM, Z K <zkaufman@nmr.mgh.harvard.edu
<mailto:zkaufman@nmr.mgh.harvard.edu>> wrote:

Hello Erin,

libreadline.so is not distributed as part of freesurfer, it should
be located somewhere on your system. For example, on CentOS 64bit
platforms it can be found in the "/lib64" directory. And on 32bit
platforms it can be found in the "/usr/lib" directory. Do you see
anything that looks like libreadline.so in either of those
directories on your system"?

-Zeke

On 05/24/2013 03:44 PM, Erin W. E. Dickie wrote:

Hello,

I just added version 5.3 to our system and am trying run
recon-all on
our dataset but it seems to be failing for all subjects pretty
early.
The only error I see is in the output (below) is:
"bc: error while loading shared libraries: libreadline.so.5:
cannot open
shared object file: No such file or directory". Is libreadline.so.5
supposed to be a part of the freesurfer package? Or is it
something that
should already exist on most systems? If its a later than I will
speak
to our system admins.

Thank you,
Erin

Fri May 24 13:58:33 EDT 2013
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618
/home/t/tpaus/raleong/__freesurfer/bin/recon-all
-subject fam1002_122618 -i
/scratch/t/tpaus/edickie/slsj___parents_T1Wc/fam1002_122618/__fam1002_122618_T1Wsc.nii
-sd
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/ -all
subjid fam1002_122618
setenv SUBJECTS_DIR
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524
FREESURFER_HOME /home/t/tpaus/raleong/__freesurfer
Actual FREESURFER_HOME /home/t/tpaus/raleong/__freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86___64-stable-pub-v5.3.0

Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13
00:26:49
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 10240 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 20000
memorylocked unlimited
maxproc 257772

total used free shared buffers
cached
Mem: 33002388 2099240 30903148 0 0
508072
-/+ buffers/cache: 1591168 31411220
Swap: 0 0 0

##############################__##########

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: 2013/05/24-17:58:33-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05
21:55:16 mreuter Exp $ User: edickie Machine: gpc-f146n031
Platform:
Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
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:
2013/05/24-17:58:33-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v
1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: edickie Machine:
gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:33-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mri_make_uchar.c,v 1.4
2011/03/02 00:04:14 nicks Exp $ User: edickie Machine:
gpc-f146n031
Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64
CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info
ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1
2012/10/17
19:11:32 nicks Exp $ User: edickie Machine: gpc-f146n031
Platform:
Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info
ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1
2011/11/08
22:18:44 nicks Exp $ User: edickie Machine: gpc-f146n031
Platform:
Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02
00:04:16
nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux
PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info
ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02
00:04:24
nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux
PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:34-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mri_label2label.c,v
1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: edickie Machine:
gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400

======= NUMBER OF OPENMP THREADS = 1 =======
ProgramName: mri_em_register ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:34-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mri_em_register.c,v
1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: edickie Machine:
gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:35-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mri_ca_normalize.c,v
1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: edickie Machine:
gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:35-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mri_ca_register.c,v
1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: edickie Machine:
gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info
ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28
22:11:20 nicks Exp $ User: edickie Machine: gpc-f146n031
Platform:
Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info
ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02
00:04:23
nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux
PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16
21:23:49
nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux
PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:36-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mri_tessellate.c,v
1.36 2011/03/02 00:04:25 nicks Exp $ User: edickie Machine:
gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:36-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User:
edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:36-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mri_normalize_tp2.c,v
1.8 2011/03/02 00:04:23 nicks Exp $ User: edickie Machine:
gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info
ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02
00:04:34
nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux
PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info
ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02
00:04:32 nicks Exp $ User: edickie Machine: gpc-f146n031
Platform:
Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:36-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mris_curvature.c,v
1.31 2011/03/02 00:04:30 nicks Exp $ User: edickie Machine:
gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info
ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02
00:04:34
nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux
PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:37-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mris_fix_topology.c,v
1.48 2011/03/02 00:04:32 nicks Exp $ User: edickie Machine:
gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:37-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mris_topo_fixer.cpp,v
1.29 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine:
gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info
ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02
00:04:27 nicks Exp $ User: edickie Machine: gpc-f146n031
Platform:
Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:37-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mris_euler_number.c,v
1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: edickie Machine:
gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:37-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mris_make_surfaces.c,v
1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: edickie Machine:
gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info
ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02
00:04:33 nicks Exp $ User: edickie Machine: gpc-f146n031
Platform:
Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info
ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02
00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031
Platform:
Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:38-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $
User:
edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info
ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02
00:04:35
nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux
PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:39-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User:
edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28
17:05:17 greve Exp $ User: edickie Machine: gpc-f146n031
Platform:
Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47
mreuter Exp $

ProgramName: mri_robust_register ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:39-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
User: edickie Machine: gpc-f146n031 Platform: Linux
PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06
mreuter Exp $

ProgramName: mri_robust_template ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:39-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
User: edickie Machine: gpc-f146n031 Platform: Linux
PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13
nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux
PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info
ProgramVersion: $Name:
stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp:
May 13
2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13
nicks Exp $
User: edickie Machine: gpc-f146n031 Platform: Linux
PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp:
2013/05/24-17:58:40-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id:
mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $
User:
edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion:
2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info
ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/05/24-17:58:40-GMT
BuildTimeStamp:
May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16
00:09:33 greve Exp $ User: edickie Machine: gpc-f146n031
Platform:
Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC
CompilerVersion: 40400
##############################__#########
GCADIR /home/t/tpaus/raleong/__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/t/tpaus/raleong/__freesurfer/average
GCS curvature.buckner40.filled.__desikan_killiany.2010-03-25.__gcs
##############################__#########
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618

mri_convert
/scratch/t/tpaus/edickie/slsj___parents_T1Wc/fam1002_122618/__fam1002_122618_T1Wsc.nii
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig/001.__mgz

mri_convert
/scratch/t/tpaus/edickie/slsj___parents_T1Wc/fam1002_122618/__fam1002_122618_T1Wsc.nii
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig/001.__mgz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/scratch/t/tpaus/edickie/slsj___parents_T1Wc/fam1002_122618/__fam1002_122618_T1Wsc.nii...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998083, -0.0436341, -0.0438852)
j_ras = (0.0442841, 0.998922, 0.0139487)
k_ras = (0.0432293, -0.0158654, 0.998939)
writing to
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig/001.__mgz...
#-----------------------------__---------------

#@# MotionCor Fri May 24 13:58:59 EDT 2013
Found 1 runs
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/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
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig/001.__mgz
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/rawavg.mgz

/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618

mri_convert
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/rawavg.mgz
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig.mgz
--conform

mri_convert
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/rawavg.mgz
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig.mgz

--conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/rawavg.mgz.__..

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998083, -0.0436341, -0.0438852)
j_ras = (0.0442841, 0.998922, 0.0139487)
k_ras = (0.0432293, -0.0158654, 0.998939)
Original Data has (1, 0.5, 0.5) mm size and (192, 512, 350) 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
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig.mgz...

mri_add_xform_to_header -c
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/transforms/__talairach.xfm
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig.mgz
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig.mgz

INFO: extension is mgz
#-----------------------------__---------------

#@# Talairach Fri May 24 13:59:31 EDT 2013
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/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

cp transforms/talairach.auto.xfm transforms/talairach.xfm

#-----------------------------__---------------

#@# Talairach Failure Detection Fri May 24 14:00:51 EDT 2013
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

talairach_afd: Talairach Transform: transforms/talairach.xfm OK
(p=0.7230, pval=0.4932 >= threshold=0.0050)

awk -f
/home/t/tpaus/raleong/__freesurfer/bin/extract___talairach_avi_QA.awk
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/transforms/__talairach_avi.log

tal_QC_AZS
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/transforms/__talairach_avi.log

TalAviQA: 0.97680
z-score:
#-----------------------------__---------------

#@# Nu Intensity Correction Fri May 24 14:00:52 EDT 2013

mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar
transforms/talairach.xfm --n 2

/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri
/home/t/tpaus/raleong/__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 gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13
00:26:49
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Fri May 24 14:00:52 EDT 2013
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
tmpdir is ./tmp.mri_nu_correct.mni.9181
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/__nu0.mnc
-odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/__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, 5.2969e-09, 3.72529e-09)
j_ras = (0, 3.72529e-09, -1)
k_ras = (-1.57161e-09, 1, -1.86265e-09)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.9181/__nu0.mnc...
------------------------------__--------------------------

Iteration 1 Fri May 24 14:00:54 EDT 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/__nu0.mnc
./tmp.mri_nu_correct.mni.9181/__nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.9181/__0/
[edickie@gpc-f146n031:/__scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/]

[2013-05-24 14:00:54] running:

/home/t/tpaus/raleong/__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.9181/__0/
./tmp.mri_nu_correct.mni.9181/__nu0.mnc
./tmp.mri_nu_correct.mni.9181/__nu1.imp

Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done

Number of iterations: 14
CV of field change: 0.000993178
[edickie@gpc-f146n031:/__scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/]

[2013-05-24 14:01:05] running:
/home/t/tpaus/raleong/__freesurfer/mni/bin/make___template
-quiet -shrink
3 ./tmp.mri_nu_correct.mni.9181/__nu0.mnc
./tmp.mri_nu_correct.mni.9181/__0//template.mnc

Transforming
slices:.......................__..............................__..............................__...Done
Transforming
slices:.......................__..............................__..............................__..............................__..............................__..............................__..............................__..............................__.......................Done
------------------------------__--------------------------

Iteration 2 Fri May 24 14:01:10 EDT 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/__nu1.mnc
./tmp.mri_nu_correct.mni.9181/__nu2.mnc -tmpdir
./tmp.mri_nu_correct.mni.9181/__1/
[edickie@gpc-f146n031:/__scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/]

[2013-05-24 14:01:10] running:

/home/t/tpaus/raleong/__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.9181/__1/
./tmp.mri_nu_correct.mni.9181/__nu1.mnc
./tmp.mri_nu_correct.mni.9181/__nu2.imp

Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done
Processing:...................__..............................__................Done

Number of iterations: 12
CV of field change: 0.000932884
[edickie@gpc-f146n031:/__scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/]

[2013-05-24 14:01:20] running:
/home/t/tpaus/raleong/__freesurfer/mni/bin/make___template
-quiet -shrink
3 ./tmp.mri_nu_correct.mni.9181/__nu1.mnc
./tmp.mri_nu_correct.mni.9181/__1//template.mnc

Transforming
slices:.......................__..............................__..............................__...Done
Transforming
slices:.......................__..............................__..............................__..............................__..............................__..............................__..............................__..............................__.......................Done
mri_binarize --i ./tmp.mri_nu_correct.mni.9181/__nu2.mnc --min
-1 --o
./tmp.mri_nu_correct.mni.9181/__ones.mgz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd
/scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.9181/__nu2.mnc
--min -1
--o ./tmp.mri_nu_correct.mni.9181/__ones.mgz

sysname Linux
hostname gpc-f146n031
machine x86_64
user edickie

input ./tmp.mri_nu_correct.mni.9181/__nu2.mnc

frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.9181/__ones.mgz

Binarizing based on threshold
min -1
max +infinity
binval 1
binvalnot 0
Found 16777216 values in range
Counting number of voxels
Found 16777216 voxels in final mask
mri_binarize done
mri_segstats --id 1 --seg
./tmp.mri_nu_correct.mni.9181/__ones.mgz --i
orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/__sum.junk --avgwf
./tmp.mri_nu_correct.mni.9181/__input.mean.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg
./tmp.mri_nu_correct.mni.9181/__ones.mgz
--i orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/__sum.junk --avgwf
./tmp.mri_nu_correct.mni.9181/__input.mean.dat

sysname Linux
hostname gpc-f146n031
machine x86_64
user edickie
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.9181/__ones.mgz

Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
0 1 16777216
16777216.000

Reporting on 1 segmentations
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.9181/__input.mean.dat

mri_segstats done
mri_segstats --id 1 --seg
./tmp.mri_nu_correct.mni.9181/__ones.mgz --i
./tmp.mri_nu_correct.mni.9181/__nu2.mnc --sum
./tmp.mri_nu_correct.mni.9181/__sum.junk --avgwf
./tmp.mri_nu_correct.mni.9181/__output.mean.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg
./tmp.mri_nu_correct.mni.9181/__ones.mgz
--i ./tmp.mri_nu_correct.mni.9181/__nu2.mnc --sum
./tmp.mri_nu_correct.mni.9181/__sum.junk --avgwf
./tmp.mri_nu_correct.mni.9181/__output.mean.dat

sysname Linux
hostname gpc-f146n031
machine x86_64
user edickie
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.9181/__ones.mgz
Loading ./tmp.mri_nu_correct.mni.9181/__nu2.mnc

Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
0 1 16777216
16777216.000

Reporting on 1 segmentations
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.9181/__output.mean.dat

mri_segstats done
bc: error while loading shared libraries: libreadline.so.5:
cannot open
shared object file: No such file or directory
mris_calc -o ./tmp.mri_nu_correct.mni.9181/__nu2.mnc
./tmp.mri_nu_correct.mni.9181/__nu2.mnc mul

Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13
00:26:49
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s fam1002_122618 exited with ERRORS at Fri May 24
14:01:44
EDT 2013

To report a problem, see
http://surfer.nmr.mgh.harvard.__edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

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