Fri Apr 5 18:06:14 CDT 2019 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27 /home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/FreeSurfer/custom/recon-all.v6.hires -subjid NSI_27 -sd /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w -all -i /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz -T2 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T2w_acpc_dc_restore.nii.gz -emregmask /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_brain.nii.gz -T2pial -openmp 8 -conf2hires subjid NSI_27 setenv SUBJECTS_DIR /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w FREESURFER_HOME /home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6 Actual FREESURFER_HOME /home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux fsl 4.4.0-142-generic #168~14.04.1-Ubuntu SMP Sat Jan 19 11:26:28 UTC 2019 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 514029 maxlocks unlimited maxsignal 514029 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 131691112 128643524 3047588 52028 37652832 85154680 -/+ buffers/cache: 5836012 125855100 Swap: 1998952 664 1998288 ######################################## program versions used $Id: recon-all,v 1.580.2.15 2016/12/08 22:02:41 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: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-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: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-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: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-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: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-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: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:14-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:15-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:15-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/04/05-23:06:15-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: functionalspinelab Machine: fsl Platform: Linux PlatformVersion: 4.4.0-142-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6/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 /home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27 mri_convert /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/001.mgz mri_convert.bin /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz... TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Fri Apr 5 18:06:30 CDT 2019 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27 mri_convert --no_scale 1 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T2w_acpc_dc_restore.nii.gz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/T2raw.mgz mri_convert.bin --no_scale 1 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T2w_acpc_dc_restore.nii.gz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/T2raw.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T2w_acpc_dc_restore.nii.gz... TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Fri Apr 5 18:06:45 CDT 2019 Found 1 runs /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/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 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig/001.mgz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/rawavg.mgz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27 mri_convert /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/rawavg.mgz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz --conform mri_convert.bin /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/rawavg.mgz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/rawavg.mgz... TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz... mri_add_xform_to_header -c /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/transforms/talairach.xfm /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz INFO: extension is mgz mri_vol2vol --mov /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_brain.nii.gz --targ /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz --regheader --interp nearest --o /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/extern.emreg.mask.mgz movvol /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_brain.nii.gz targvol /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/orig.mgz outvol /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/extern.emreg.mask.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1554748358 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 -0.00001; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.42857 0.00000 0.00000 -52.85715; 0.00000 0.00000 1.42857 -27.35713; 0.00000 -1.42857 0.00000 312.85715; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done #-------------------------------------------- #@# Talairach Fri Apr 5 18:07:00 CDT 2019 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri /home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6/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 fsl 4.4.0-142-generic #168~14.04.1-Ubuntu SMP Sat Jan 19 11:26:28 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Fri Apr 5 18:07:00 CDT 2019 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.30912 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30912/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.30912/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.30912/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Fri Apr 5 18:07:13 CDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.30912/nu0.mnc ./tmp.mri_nu_correct.mni.30912/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30912/0/ -iterations 1000 -distance 50 [functionalspinelab@fsl:/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27/mri/] [2019-04-05 18:07:13] running: /home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6/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.30912/0/ ./tmp.mri_nu_correct.mni.30912/nu0.mnc ./tmp.mri_nu_correct.mni.30912/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 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: 35 CV of field change: 0.000990652 Outputting Volume: ............................................................ Outputting Volume: ............................................................ minc_modify_header: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed. nu_evaluate: crashed while running minc_modify_header (termination status=134) nu_correct: crashed while running nu_evaluate (termination status=65280) ERROR: nu_correct Linux fsl 4.4.0-142-generic #168~14.04.1-Ubuntu SMP Sat Jan 19 11:26:28 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s NSI_27 exited with ERRORS at Fri Apr 5 18:08:55 CDT 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting