‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۶:۰۲ (+0430)‬ /home/nazanin/freesurfer/subjects/khameh /home/nazanin/freesurfer/bin/recon-all -i khameh1.nii -s khameh -autorecon1 subjid khameh setenv SUBJECTS_DIR /home/nazanin/freesurfer/subjects FREESURFER_HOME /home/nazanin/freesurfer Actual FREESURFER_HOME /home/nazanin/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux nazanin-Aspire-V3-571G 4.15.0-76-generic #86-Ubuntu SMP Fri Jan 17 17:24:28 UTC 2020 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 16384 kbytes maxproc 23236 maxlocks unlimited maxsignal 23236 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 5993296 1051208 2255352 317668 2686736 4325436 Swap: 4999164 0 4999164 ######################################## 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: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-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: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-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: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-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: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-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: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/07/01-09:16:02-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: nazanin Machine: nazanin-Aspire-V3-571G Platform: Linux PlatformVersion: 4.15.0-76-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/nazanin/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 /home/nazanin/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/nazanin/freesurfer/subjects/khameh mri_convert /home/nazanin/khameh1.nii /home/nazanin/freesurfer/subjects/khameh/mri/orig/001.mgz mri_convert.bin /home/nazanin/khameh1.nii /home/nazanin/freesurfer/subjects/khameh/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/nazanin/khameh1.nii... TR=8.16, 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 /home/nazanin/freesurfer/subjects/khameh/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor ‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۶:۰۶ (+0430)‬ Found 1 runs /home/nazanin/freesurfer/subjects/khameh/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 /home/nazanin/freesurfer/subjects/khameh/mri/orig/001.mgz /home/nazanin/freesurfer/subjects/khameh/mri/rawavg.mgz /home/nazanin/freesurfer/subjects/khameh mri_convert /home/nazanin/freesurfer/subjects/khameh/mri/rawavg.mgz /home/nazanin/freesurfer/subjects/khameh/mri/orig.mgz --conform mri_convert.bin /home/nazanin/freesurfer/subjects/khameh/mri/rawavg.mgz /home/nazanin/freesurfer/subjects/khameh/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/nazanin/freesurfer/subjects/khameh/mri/rawavg.mgz... TR=8.16, 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 /home/nazanin/freesurfer/subjects/khameh/mri/orig.mgz... mri_add_xform_to_header -c /home/nazanin/freesurfer/subjects/khameh/mri/transforms/talairach.xfm /home/nazanin/freesurfer/subjects/khameh/mri/orig.mgz /home/nazanin/freesurfer/subjects/khameh/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach ‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۶:۱۶ (+0430)‬ /home/nazanin/freesurfer/subjects/khameh/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/nazanin/freesurfer/subjects/khameh/mri /home/nazanin/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 nazanin-Aspire-V3-571G 4.15.0-76-generic #86-Ubuntu SMP Fri Jan 17 17:24:28 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux ‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۶:۱۶ (+0430)‬ 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.10109 /home/nazanin/freesurfer/subjects/khameh/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10109/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10109/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=8.16, 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.10109/nu0.mnc... -------------------------------------------------------- Iteration 1 ‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۶:۱۸ (+0430)‬ nu_correct -clobber ./tmp.mri_nu_correct.mni.10109/nu0.mnc ./tmp.mri_nu_correct.mni.10109/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10109/0/ -iterations 1000 -distance 50 [nazanin@nazanin-Aspire-V3-571G:/home/nazanin/freesurfer/subjects/khameh/mri/] [2020-07-01 13:46:18] running: /home/nazanin/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.10109/0/ ./tmp.mri_nu_correct.mni.10109/nu0.mnc ./tmp.mri_nu_correct.mni.10109/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 Number of iterations: 34 CV of field change: 0.000994534 mri_convert ./tmp.mri_nu_correct.mni.10109/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.10109/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.10109/nu1.mnc... TR=0.00, 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) 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... ‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۷:۱۱ (+0430)‬ 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 ‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۷:۱۱ (+0430)‬ Ended at ‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۷:۴۳ (+0430)‬ talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection ‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۷:۴۵ (+0430)‬ /home/nazanin/freesurfer/subjects/khameh/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8324, pval=0.9628 >= threshold=0.0050) awk -f /home/nazanin/freesurfer/bin/extract_talairach_avi_QA.awk /home/nazanin/freesurfer/subjects/khameh/mri/transforms/talairach_avi.log tal_QC_AZS /home/nazanin/freesurfer/subjects/khameh/mri/transforms/talairach_avi.log TalAviQA: 0.97817 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction ‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۷:۴۵ (+0430)‬ mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/nazanin/freesurfer/subjects/khameh/mri /home/nazanin/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 nazanin-Aspire-V3-571G 4.15.0-76-generic #86-Ubuntu SMP Fri Jan 17 17:24:28 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux ‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۷:۴۵ (+0430)‬ 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.10801 /home/nazanin/freesurfer/subjects/khameh/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10801/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10801/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=8.16, 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.10801/nu0.mnc... -------------------------------------------------------- Iteration 1 ‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۷:۴۷ (+0430)‬ nu_correct -clobber ./tmp.mri_nu_correct.mni.10801/nu0.mnc ./tmp.mri_nu_correct.mni.10801/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10801/0/ [nazanin@nazanin-Aspire-V3-571G:/home/nazanin/freesurfer/subjects/khameh/mri/] [2020-07-01 13:47:47] running: /home/nazanin/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.10801/0/ ./tmp.mri_nu_correct.mni.10801/nu0.mnc ./tmp.mri_nu_correct.mni.10801/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 Number of iterations: 25 CV of field change: 0.000984301 -------------------------------------------------------- Iteration 2 ‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۸:۲۱ (+0430)‬ nu_correct -clobber ./tmp.mri_nu_correct.mni.10801/nu1.mnc ./tmp.mri_nu_correct.mni.10801/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.10801/1/ [nazanin@nazanin-Aspire-V3-571G:/home/nazanin/freesurfer/subjects/khameh/mri/] [2020-07-01 13:48:21] running: /home/nazanin/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.10801/1/ ./tmp.mri_nu_correct.mni.10801/nu1.mnc ./tmp.mri_nu_correct.mni.10801/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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 18 CV of field change: 0.000986883 mri_binarize --i ./tmp.mri_nu_correct.mni.10801/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10801/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /home/nazanin/freesurfer/subjects/khameh/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.10801/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10801/ones.mgz sysname Linux hostname nazanin-Aspire-V3-571G machine x86_64 user nazanin input ./tmp.mri_nu_correct.mni.10801/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.10801/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.10801/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10801/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10801/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.10801/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10801/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10801/input.mean.dat sysname Linux hostname nazanin-Aspire-V3-571G machine x86_64 user nazanin UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10801/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.10801/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10801/ones.mgz --i ./tmp.mri_nu_correct.mni.10801/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10801/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10801/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.10801/ones.mgz --i ./tmp.mri_nu_correct.mni.10801/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10801/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10801/output.mean.dat sysname Linux hostname nazanin-Aspire-V3-571G machine x86_64 user nazanin UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10801/ones.mgz Loading ./tmp.mri_nu_correct.mni.10801/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.10801/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.10801/nu2.mnc ./tmp.mri_nu_correct.mni.10801/nu2.mnc mul 1.04690219383331921019 Saving result to './tmp.mri_nu_correct.mni.10801/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.10801/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.10801/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.10801/nu2.mnc... TR=0.00, 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) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz mghRead(/home/nazanin/freesurfer/subjects/khameh/mri/nu.mgz): could not read 262144 bytes at slice 45 No such file or directory mri_make_uchar: could not read input volume nu.mgz No space left on device Linux nazanin-Aspire-V3-571G 4.15.0-76-generic #86-Ubuntu SMP Fri Jan 17 17:24:28 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s khameh exited with ERRORS at ‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۹:۱۰ (+0430)‬ To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting