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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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