Re: [Freesurfer] problem with libreadline.so.5

24 May 2013

      I get this....
lrwxrwxrwx 1 root root     18 May  4 09:49 libreadline.so.5 ->
libreadline.so.5.2
-rwxr-xr-x 1 root root 261144 Nov 10  2010 libreadline.so.5.2
lrwxrwxrwx 1 root root     18 May  4 09:49 libreadline.so.6 ->
libreadline.so.6.0
-rwxr-xr-x 1 root root 269592 Jun 22  2012 libreadline.so.6.0
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 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

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    https://mail.nmr.mgh.harvard._**_edu/mailman/listinfo/__**

freesurfer
    <https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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Re: [Freesurfer] problem with libreadline.so.5