Sun Jun 4 21:09:32 IST 2017 /mnt/research/freesurfer_analysis/subjects/grp127 /usr/local/freesurfer/bin/recon-all -all -i grp127_t1.nii -s grp127 -sd subjects -use-gpu subjid grp127 setenv SUBJECTS_DIR /mnt/research/freesurfer_analysis/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux rameshbabu 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63592 maxlocks unlimited maxsignal 63592 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16326760 2320264 11793924 33172 2212572 13636640 Swap: 16669692 0 16669692 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/04-15:39:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: rb Machine: rameshbabu Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /mnt/research/freesurfer_analysis/subjects/grp127 mri_convert /mnt/research/freesurfer_analysis/grp127_t1.nii /mnt/research/freesurfer_analysis/subjects/grp127/mri/orig/001.mgz mri_convert.bin /mnt/research/freesurfer_analysis/grp127_t1.nii /mnt/research/freesurfer_analysis/subjects/grp127/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/research/freesurfer_analysis/grp127_t1.nii... TR=7.55, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0395902, -0.986362, 0.159759) j_ras = (0.0125947, 0.160364, 0.986978) k_ras = (0.999137, 0.0370625, -0.0187718) writing to /mnt/research/freesurfer_analysis/subjects/grp127/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Jun 4 21:09:36 IST 2017 Found 1 runs /mnt/research/freesurfer_analysis/subjects/grp127/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 /mnt/research/freesurfer_analysis/subjects/grp127/mri/orig/001.mgz /mnt/research/freesurfer_analysis/subjects/grp127/mri/rawavg.mgz /mnt/research/freesurfer_analysis/subjects/grp127 mri_convert /mnt/research/freesurfer_analysis/subjects/grp127/mri/rawavg.mgz /mnt/research/freesurfer_analysis/subjects/grp127/mri/orig.mgz --conform mri_convert.bin /mnt/research/freesurfer_analysis/subjects/grp127/mri/rawavg.mgz /mnt/research/freesurfer_analysis/subjects/grp127/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/research/freesurfer_analysis/subjects/grp127/mri/rawavg.mgz... TR=7.55, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0395902, -0.986362, 0.159759) j_ras = (0.0125947, 0.160364, 0.986978) k_ras = (0.999137, 0.0370625, -0.0187718) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/research/freesurfer_analysis/subjects/grp127/mri/orig.mgz... mri_add_xform_to_header -c /mnt/research/freesurfer_analysis/subjects/grp127/mri/transforms/talairach.xfm /mnt/research/freesurfer_analysis/subjects/grp127/mri/orig.mgz /mnt/research/freesurfer_analysis/subjects/grp127/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sun Jun 4 21:09:48 IST 2017 /mnt/research/freesurfer_analysis/subjects/grp127/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /mnt/research/freesurfer_analysis/subjects/grp127/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux rameshbabu 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sun Jun 4 21:09:48 IST 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.8829 /mnt/research/freesurfer_analysis/subjects/grp127/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.8829/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.8829/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=7.55, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 0) j_ras = (1.86265e-09, -2.03145e-08, -1) k_ras = (-3.72529e-09, 1, -9.66247e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.8829/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Jun 4 21:09:53 IST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.8829/nu0.mnc ./tmp.mri_nu_correct.mni.8829/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8829/0/ -iterations 1000 -distance 50 [rb@rameshbabu:/mnt/research/freesurfer_analysis/subjects/grp127/mri/] [2017-06-04 21:09:53] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.8829/0/ ./tmp.mri_nu_correct.mni.8829/nu0.mnc ./tmp.mri_nu_correct.mni.8829/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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 23 CV of field change: 0.000966215 mri_convert ./tmp.mri_nu_correct.mni.8829/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.8829/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.8829/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 0) j_ras = (1.86265e-09, -2.03145e-08, -1) k_ras = (-3.72529e-09, 1, -9.66247e-09) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Sun Jun 4 21:10:42 IST 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sun Jun 4 21:10:42 IST 2017 Ended at Sun Jun 4 21:11:18 IST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sun Jun 4 21:11:20 IST 2017 /mnt/research/freesurfer_analysis/subjects/grp127/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7581, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /mnt/research/freesurfer_analysis/subjects/grp127/mri/transforms/talairach_avi.log tal_QC_AZS /mnt/research/freesurfer_analysis/subjects/grp127/mri/transforms/talairach_avi.log TalAviQA: 0.97584 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sun Jun 4 21:11:20 IST 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /mnt/research/freesurfer_analysis/subjects/grp127/mri /usr/local/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 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux rameshbabu 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sun Jun 4 21:11:20 IST 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.10582 /mnt/research/freesurfer_analysis/subjects/grp127/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10582/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10582/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=7.55, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 0) j_ras = (1.86265e-09, -2.03145e-08, -1) k_ras = (-3.72529e-09, 1, -9.66247e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.10582/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Jun 4 21:11:23 IST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.10582/nu0.mnc ./tmp.mri_nu_correct.mni.10582/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10582/0/ [rb@rameshbabu:/mnt/research/freesurfer_analysis/subjects/grp127/mri/] [2017-06-04 21:11:23] running: /usr/local/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.10582/0/ ./tmp.mri_nu_correct.mni.10582/nu0.mnc ./tmp.mri_nu_correct.mni.10582/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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 18 CV of field change: 0.000933992 -------------------------------------------------------- Iteration 2 Sun Jun 4 21:11:50 IST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.10582/nu1.mnc ./tmp.mri_nu_correct.mni.10582/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.10582/1/ [rb@rameshbabu:/mnt/research/freesurfer_analysis/subjects/grp127/mri/] [2017-06-04 21:11:50] running: /usr/local/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.10582/1/ ./tmp.mri_nu_correct.mni.10582/nu1.mnc ./tmp.mri_nu_correct.mni.10582/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 8 CV of field change: 0.00098157 mri_binarize --i ./tmp.mri_nu_correct.mni.10582/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10582/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /mnt/research/freesurfer_analysis/subjects/grp127/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.10582/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10582/ones.mgz sysname Linux hostname rameshbabu machine x86_64 user rb input ./tmp.mri_nu_correct.mni.10582/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.10582/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10582/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10582/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10582/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10582/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10582/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10582/input.mean.dat sysname Linux hostname rameshbabu machine x86_64 user rb UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10582/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.10582/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10582/ones.mgz --i ./tmp.mri_nu_correct.mni.10582/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10582/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10582/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10582/ones.mgz --i ./tmp.mri_nu_correct.mni.10582/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10582/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10582/output.mean.dat sysname Linux hostname rameshbabu machine x86_64 user rb UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10582/ones.mgz Loading ./tmp.mri_nu_correct.mni.10582/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.10582/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.10582/nu2.mnc ./tmp.mri_nu_correct.mni.10582/nu2.mnc mul 1.01259899107946931825 Saving result to './tmp.mri_nu_correct.mni.10582/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.10582/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.10582/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.10582/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 0) j_ras = (1.86265e-09, -2.03145e-08, -1) k_ras = (-3.72529e-09, 1, -9.66247e-09) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping ( 5, 141) to ( 3, 110) Sun Jun 4 21:12:48 IST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /mnt/research/freesurfer_analysis/subjects/grp127/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sun Jun 4 21:12:49 IST 2017 /mnt/research/freesurfer_analysis/subjects/grp127/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.18723 0.01770 0.00295 0.21379; 0.00792 1.24726 0.07902 3.01236; 0.02841 -0.10039 1.18746 2.92110; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 11 Starting OpenSpline(): npoints = 11 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 63 (63), valley at 36 (36) csf peak at 31, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 65 (65), valley at 37 (37) csf peak at 33, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 28 seconds. #-------------------------------------------- #@# Skull Stripping Sun Jun 4 21:14:17 IST 2017 /mnt/research/freesurfer_analysis/subjects/grp127/mri mri_em_register_cuda -rusage /mnt/research/freesurfer_analysis/subjects/grp127/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 8.0 Runtime : 5.0 Acquiring CUDA device Using default device CUDA device: GeForce GT 610 aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register_cuda for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=8.0 skull bounding box = (60, 47, 37) --> (200, 255, 209) using (107, 116, 123) as brain centroid... mean wm in atlas = 108, using box (90,90,102) --> (124, 141,144) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 107 +- 5.3 after smoothing, mri peak at 107, scaling input intensities by 1.009 scaling channel 0 by 1.00935 initial log_p = -14795.762 ************************************************ First Search limited to translation only. ************************************************ max log p = -14805.583984 @ (0.000, 0.000, 0.000) max log p = -14569.646484 @ (-4.545, -13.636, -13.636) max log p = -14389.634766 @ (2.273, 6.818, 2.273) max log p = -14337.971680 @ (-1.136, 1.136, 1.136) max log p = -14292.050781 @ (1.705, -0.568, -0.568) max log p = -14292.050781 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -6.3, -10.8): log p = -4.407 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** find_optimal_linear_xform: Starting reduction 0 find_optimal_linear_xform: Starting reduction 1 Result so far: scale 1.000: max_log_p=-12497.023, old_max_log_p =-4.407 (thresh=-4.4) 1.15000 0.00000 0.00000 -20.69151; 0.00000 1.14016 0.15011 -37.82396; 0.00000 -0.16136 1.22567 -14.31398; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** find_optimal_linear_xform: Starting reduction 0 find_optimal_linear_xform: Starting reduction 1 Result so far: scale 0.250: max_log_p=-12113.641, old_max_log_p =-12497.023 (thresh=-12484.5) 1.17156 0.00000 0.00000 -27.24120; 0.00000 1.21367 0.07359 -37.13567; 0.00000 -0.08483 1.20975 -23.25438; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** find_optimal_linear_xform: Starting reduction 0 find_optimal_linear_xform: Starting reduction 1 Result so far: scale 0.250: max_log_p=-12102.920, old_max_log_p =-12113.641 (thresh=-12101.5) 1.19289 0.04045 0.00245 -34.11225; -0.03905 1.23577 0.07493 -35.32948; 0.00000 -0.08324 1.18707 -20.73855; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** find_optimal_linear_xform: Starting reduction 0 find_optimal_linear_xform: Starting reduction 1 Result so far: scale 0.062: max_log_p=-12055.082, old_max_log_p =-12102.920 (thresh=-12090.8) 1.19624 0.01115 -0.00951 -29.45969; -0.00986 1.23280 0.08405 -40.22091; 0.01021 -0.09286 1.18640 -21.08548; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** find_optimal_linear_xform: Starting reduction 0 find_optimal_linear_xform: Starting reduction 1 Result so far: scale 0.062: max_log_p=-12055.082, old_max_log_p =-12055.082 (thresh=-12043.0) 1.19624 0.01115 -0.00951 -29.45969; -0.00986 1.23280 0.08405 -40.22091; 0.01021 -0.09286 1.18640 -21.08548; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.19624 0.01115 -0.00951 -29.45969; -0.00986 1.23280 0.08405 -40.22091; 0.01021 -0.09286 1.18640 -21.08548; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.19624 0.01115 -0.00951 -29.45969; -0.00986 1.23280 0.08405 -40.22091; 0.01021 -0.09286 1.18640 -21.08548; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.19624 0.01115 -0.00951 -29.45969; -0.00986 1.23280 0.08405 -40.22091; 0.01021 -0.09286 1.18640 -21.08548; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.717 (old=-4.562) transform before final EM align: 1.19624 0.01115 -0.00951 -29.45969; -0.00986 1.23280 0.08405 -40.22091; 0.01021 -0.09286 1.18640 -21.08548; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.19624 0.01115 -0.00951 -29.45969; -0.00986 1.23280 0.08405 -40.22091; 0.01021 -0.09286 1.18640 -21.08548; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.19624 0.01115 -0.00951 -29.45969; -0.00986 1.23280 0.08405 -40.22091; 0.01021 -0.09286 1.18640 -21.08548; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = 4.1 tol 0.000000 final transform: 1.19624 0.01115 -0.00951 -29.45969; -0.00986 1.23280 0.08405 -40.22091; 0.01021 -0.09286 1.18640 -21.08548; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 291.444000 mri_em_register stimesec 306.092000 mri_em_register ru_maxrss 704508 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 198111 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 3706223 mri_em_register ru_nivcsw 1060 registration took 26 minutes and 45 seconds. mri_watershed -rusage /mnt/research/freesurfer_analysis/subjects/grp127/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=122 z=119 r=82 first estimation of the main basin volume: 2366886 voxels Looking for seedpoints 2 found in the cerebellum 13 found in the rest of the brain global maximum in x=155, y=114, z=88, Imax=255 CSF=16, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=414233911 voxels, voxel volume =1.000 = 414233911 mmm3 = 414233.920 cm3 done. PostAnalyze...Basin Prior 2 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=129,y=122, z=114, r=8550 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=25 , nb = 45242 RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=34 , nb = -1034208463 LEFT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=36 , nb = -1044961116 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=23 , nb = -1115971206 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=24 , nb = 1078201240 OTHER CSF_MIN=2, CSF_intensity=26, CSF_MAX=37 , nb = 1067196964 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 25, 29, 36, 60 after analyzing : 25, 33, 36, 39 RIGHT_CER before analyzing : 34, 37, 41, 65 after analyzing : 34, 39, 41, 45 LEFT_CER before analyzing : 36, 37, 40, 73 after analyzing : 36, 39, 40, 47 RIGHT_BRAIN before analyzing : 23, 27, 35, 59 after analyzing : 23, 32, 35, 38 LEFT_BRAIN before analyzing : 24, 28, 36, 60 after analyzing : 24, 33, 36, 39 OTHER before analyzing : 37, 28, 24, 30 after analyzing : 27, 28, 28, 28 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...68 iterations *********************VALIDATION********************* curvature mean = -0.015, std = 0.012 curvature mean = 62.779, std = 5.250 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.32, sigma = 4.59 after rotation: sse = 3.32, sigma = 4.59 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.46, its var is 4.02 before Erosion-Dilatation 0.32% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...36 iterations mri_strip_skull: done peeling brain Brain Size = 1232744 voxels, voxel volume = 1.000 mm3 = 1232744 mmm3 = 1232.744 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 17.248000 mri_watershed stimesec 0.204000 mri_watershed ru_maxrss 832048 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 211535 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2016 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 0 mri_watershed ru_nivcsw 31 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sun Jun 4 21:41:21 IST 2017 /mnt/research/freesurfer_analysis/subjects/grp127/mri mri_em_register_cuda -rusage /mnt/research/freesurfer_analysis/subjects/grp127/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 8.0 Runtime : 5.0 Acquiring CUDA device Using default device CUDA device: GeForce GT 610 setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register_cuda for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=28.0 skull bounding box = (69, 68, 51) --> (192, 172, 192) using (110, 103, 122) as brain centroid... mean wm in atlas = 107, using box (95,90,105) --> (125, 115,139) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 106 +- 5.0 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -11683.303 ************************************************ First Search limited to translation only. ************************************************ max log p = -11709.341797 @ (0.000, 0.000, 0.000) max log p = -11415.160156 @ (-4.545, -4.545, -4.545) max log p = -11415.160156 @ (0.000, 0.000, 0.000) max log p = -11415.160156 @ (0.000, 0.000, 0.000) max log p = -11363.703125 @ (0.568, 1.705, 1.705) max log p = -11363.703125 @ (0.000, 0.000, 0.000) Found translation: (-4.0, -2.8, -2.8): log p = -4.015 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** find_optimal_linear_xform: Starting reduction 0 find_optimal_linear_xform: Starting reduction 1 Result so far: scale 1.000: max_log_p=-9899.376, old_max_log_p =-4.015 (thresh=-4.0) 1.15000 0.00000 0.00000 -23.58442; 0.00000 1.15000 0.00000 -21.16055; 0.00000 0.00000 1.15000 -26.58368; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** find_optimal_linear_xform: Starting reduction 0 find_optimal_linear_xform: Starting reduction 1 Result so far: scale 0.250: max_log_p=-9652.092, old_max_log_p =-9899.376 (thresh=-9889.5) 1.14938 -0.03885 -0.00383 -18.31985; 0.03692 1.16449 0.11469 -40.92421; 0.00000 -0.11475 1.16512 -12.42914; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** find_optimal_linear_xform: Starting reduction 0 find_optimal_linear_xform: Starting reduction 1 Result so far: scale 0.250: max_log_p=-9632.883, old_max_log_p =-9652.092 (thresh=-9642.4) 1.17154 -0.00074 -0.00007 -26.30090; -0.00072 1.18699 0.11691 -39.00570; 0.00000 -0.11691 1.18696 -16.51426; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** find_optimal_linear_xform: Starting reduction 0 find_optimal_linear_xform: Starting reduction 1 Result so far: scale 0.250: max_log_p=-9632.883, old_max_log_p =-9632.883 (thresh=-9623.2) 1.17154 -0.00074 -0.00007 -26.30090; -0.00072 1.18699 0.11691 -39.00570; 0.00000 -0.11691 1.18696 -16.51426; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** find_optimal_linear_xform: Starting reduction 0 find_optimal_linear_xform: Starting reduction 1 Result so far: scale 0.062: max_log_p=-9556.975, old_max_log_p =-9632.883 (thresh=-9623.2) 1.16872 -0.00962 -0.01057 -23.63552; 0.00888 1.18729 0.09743 -37.59486; 0.00955 -0.09740 1.18588 -20.01996; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** find_optimal_linear_xform: Starting reduction 0 find_optimal_linear_xform: Starting reduction 1 Result so far: scale 0.062: max_log_p=-9556.975, old_max_log_p =-9556.975 (thresh=-9547.4) 1.16872 -0.00962 -0.01057 -23.63552; 0.00888 1.18729 0.09743 -37.59486; 0.00955 -0.09740 1.18588 -20.01996; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.16872 -0.00962 -0.01057 -23.63552; 0.00888 1.18729 0.09743 -37.59486; 0.00955 -0.09740 1.18588 -20.01996; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.16872 -0.00962 -0.01057 -23.63552; 0.00888 1.18729 0.09743 -37.59486; 0.00955 -0.09740 1.18588 -20.01996; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.16872 -0.00962 -0.01057 -23.63552; 0.00888 1.18729 0.09743 -37.59486; 0.00955 -0.09740 1.18588 -20.01996; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.377 (old=-4.128) transform before final EM align: 1.16872 -0.00962 -0.01057 -23.63552; 0.00888 1.18729 0.09743 -37.59486; 0.00955 -0.09740 1.18588 -20.01996; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.16872 -0.00962 -0.01057 -23.63552; 0.00888 1.18729 0.09743 -37.59486; 0.00955 -0.09740 1.18588 -20.01996; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.16872 -0.00962 -0.01057 -23.63552; 0.00888 1.18729 0.09743 -37.59486; 0.00955 -0.09740 1.18588 -20.01996; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 009: -log(p) = 3.9 after pass:transform: ( 1.17, -0.01, -0.01, -23.64) ( 0.01, 1.19, 0.10, -37.59) ( 0.01, -0.10, 1.19, -20.02) dfp_em_step_func: 010: -log(p) = 3.9 after pass:transform: ( 1.17, -0.01, -0.01, -23.64) ( 0.01, 1.19, 0.10, -37.59) ( 0.01, -0.10, 1.19, -20.02) dfp_em_step_func: 011: -log(p) = 3.9 after pass:transform: ( 1.17, -0.01, -0.01, -23.64) ( 0.01, 1.19, 0.10, -37.59) ( 0.01, -0.10, 1.19, -20.02) dfp_em_step_func: 012: -log(p) = 3.9 after pass:transform: ( 1.17, -0.01, -0.01, -23.64) ( 0.01, 1.19, 0.10, -37.59) ( 0.01, -0.10, 1.19, -20.02) pass 2 through quasi-newton minimization... outof QuasiNewtonEMA: 014: -log(p) = 3.9 tol 0.000000 final transform: 1.16914 -0.00918 -0.01019 -23.63552; 0.00897 1.18733 0.09750 -37.59486; 0.00977 -0.09712 1.18611 -20.01996; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1498.168000 mri_em_register stimesec 832.096000 mri_em_register ru_maxrss 693824 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 203979 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 4201697 mri_em_register ru_nivcsw 73662 registration took 56 minutes and 25 seconds. #-------------------------------------- #@# CA Normalize Sun Jun 4 22:37:46 IST 2017 /mnt/research/freesurfer_analysis/subjects/grp127/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=29.0 skull bounding box = (69, 68, 52) --> (192, 172, 192) using (110, 103, 122) as brain centroid... mean wm in atlas = 107, using box (95,90,105) --> (125, 115,139) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 106 +- 5.0 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 246344 sample points... INFO: compute sample coordinates transform 1.16914 -0.00918 -0.01019 -23.63552; 0.00897 1.18733 0.09750 -37.59486; 0.00977 -0.09712 1.18611 -20.01996; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 65, 49) --> (187, 164, 189) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 2030 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (75, 66, 48) --> (132, 165, 190) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 2111 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 140, 69) --> (173, 175, 115) Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0 0 of 126 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (92, 140, 68) --> (130, 175, 116) Right_Cerebellum_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 36 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (116, 131, 100) --> (146, 190, 125) Brain_Stem: limiting intensities to 89.0 --> 132.0 0 of 123 (0.0%) samples deleted using 4426 total control points for intensity normalization... bias field = 0.948 +- 0.046 27 of 4426 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 65, 49) --> (187, 164, 189) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 2623 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (75, 66, 48) --> (132, 165, 190) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 1 of 2592 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 140, 69) --> (173, 175, 115) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 45 of 236 (19.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (92, 140, 68) --> (130, 175, 116) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 22 of 113 (19.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (116, 131, 100) --> (146, 190, 125) Brain_Stem: limiting intensities to 88.0 --> 132.0 70 of 209 (33.5%) samples deleted using 5773 total control points for intensity normalization... bias field = 1.019 +- 0.040 28 of 5583 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 65, 49) --> (187, 164, 189) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 11 of 2670 (0.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (75, 66, 48) --> (132, 165, 190) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 2 of 2683 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 140, 69) --> (173, 175, 115) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 136 of 254 (53.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (92, 140, 68) --> (130, 175, 116) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 112 of 160 (70.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (116, 131, 100) --> (146, 190, 125) Brain_Stem: limiting intensities to 88.0 --> 132.0 142 of 259 (54.8%) samples deleted using 6026 total control points for intensity normalization... bias field = 1.015 +- 0.036 30 of 5485 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 15 seconds. #-------------------------------------- #@# CA Reg Sun Jun 4 22:39:00 IST 2017 /mnt/research/freesurfer_analysis/subjects/grp127/mri mri_ca_register_cuda -rusage /mnt/research/freesurfer_analysis/subjects/grp127/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 8.0 Runtime : 5.0 Acquiring CUDA device Using default device CUDA device: GeForce GT 610 not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register_cuda for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.66 (predicted orig area = 4.8) freeing gibbs priors...done. average std[0] = 5.0 AllocateHost: Warning - not thread safe! RecvAll: Did not reset gca in dst GCAMcopyNodePositions: On GPU RecvAll: Did not reset gca in dst GCAMcopyNodePositions: On GPU RecvAll: Did not reset gca in dst GCAMcopyNodePositions: On GPU RecvAll: Did not reset gca in dst RecvAll: Did not reset gca in dst RecvAll: Did not reset gca in dst GCAMcopyNodePositions: On GPU RecvAll: Did not reset gca in dst RecvAll: Did not reset gca in dst RecvAll: Did not reset gca in dst RecvAll: Did not reset gca in dst label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... GCAMregisterPipelineAndComputeRMS: On GPU 0000: dt=0.000, rms=0.824, neg=0, invalid=0 LabelTerm: Did not call MRIsetResolution PutOnGPU: Did not reset gca in dst FindOptimalTimestep: Complete in 21354.1 ms (avg) 21354.1 ms (tot) 0001: dt=179.811325, rms=0.731 (11.255%), neg=0, invalid=762 LabelTerm: Did not call MRIsetResolution PutOnGPU: Did not reset gca in dst FindOptimalTimestep: Complete in 22326.6 ms (avg) 22326.6 ms (tot) 0002: dt=123.877968, rms=0.706 (3.382%), neg=0, invalid=762 LabelTerm: Did not call MRIsetResolution PutOnGPU: Did not reset gca in dst FindOptimalTimestep: Complete in 22853.2 ms (avg) 22853.2 ms (tot) CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of memory. Abort (core dumped) ERROR: mri_ca_register with non-zero status 134 but continuing despite the error #-------------------------------------- #@# SubCort Seg Sun Jun 4 22:41:33 IST 2017 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname rameshbabu machine x86_64 setenv SUBJECTS_DIR /mnt/research/freesurfer_analysis/subjects cd /mnt/research/freesurfer_analysis/subjects/grp127/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz transforms/talairach.m3z: could not open transform average std[0] = 7.3 reading transform from transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z No such file or directory Linux rameshbabu 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s grp127 exited with ERRORS at Sun Jun 4 22:41:56 IST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting