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