Wed Nov 13 13:43:32 EST 2019 /home/dbermudez/Documents/subjects/00_0086 /usr/local/freesurfer/bin/recon-all -subjid 00_0086 -i RAW/00_0086/ns_00_0086_3T_T1w_MPR1.nii -i RAW/00_0086/ns_00_0086_3T_T1w_MPR2.nii subjid 00_0086 setenv SUBJECTS_DIR /home/dbermudez/Documents/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-local-build-dev-20191112 Linux dbermudez-XPS-15-9550 5.0.0-32-generic #34~18.04.2-Ubuntu SMP Thu Oct 10 10:36:02 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 16384 kbytes maxproc 62333 maxlocks unlimited maxsignal 62333 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16005232 2375836 10735724 212276 2893672 13070860 Swap: 2097148 0 2097148 ######################################## program versions used $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $ ProgramName: lta_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mri_annotation2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: 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mris_jacobian.c,v 1.11 2015/02/05 23:34:40 zkaufman Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mris_label2annot ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mris_left_right_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mris_left_right_register.c,v 1.2 2011/12/16 20:49:37 greve Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mris_make_surfaces.c,v 1.172 2017/02/16 19:42:36 fischl Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mris_register.c,v 1.64 2017/02/07 19:04:44 fischl Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mris_surface_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mris_surface_stats.c,v 1.10 2011/03/02 00:04:34 nicks Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mri_stats2seg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mri_stats2seg.c,v 1.9 2011/03/02 00:04:24 nicks Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mris_thickness ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mris_thickness.c,v 1.28 2012/11/27 17:41:26 fischl Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mris_thickness_diff ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mris_thickness_diff.c,v 1.16 2011/03/02 00:04:34 nicks Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mri_surf2surf ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mri_surf2vol ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mri_surf2vol.c,v 1.28 2014/12/08 19:49:02 greve Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mri_surfcluster ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mris_volmask ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mris_volmask.cpp,v 1.28 2016/11/18 19:19:29 fischl Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mri_vol2surf ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mri_vol2surf.c,v 1.68 2014/05/30 20:58:47 greve Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mri_vol2vol ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mri_vol2vol.c,v 1.89 2016/06/22 22:33:40 fischl Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mri_voldiff ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mri_voldiff.c,v 1.6 2011/03/02 00:04:25 nicks Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 ProgramName: tkregister2_cmdl ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: tkregister2.c,v 1.133 2016/08/02 21:17:11 greve Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/11/13-18:43:32-GMT BuildTimeStamp: Nov 12 2019 00:45:11 Id: $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ User: dbermudez Machine: dbermudez-XPS-15-9550 Platform: Linux PlatformVersion: 5.0.0-32-generic CompilerName: GCC CompilerVersion: 40900 FLIRT version 6.0 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 ####################################### 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 ####################################### /home/dbermudez/Documents/subjects/00_0086 mri_convert /home/dbermudez/Documents/subjects/RAW/00_0086/ns_00_0086_3T_T1w_MPR1.nii /home/dbermudez/Documents/subjects/00_0086/mri/orig/001.mgz mri_convert /home/dbermudez/Documents/subjects/RAW/00_0086/ns_00_0086_3T_T1w_MPR1.nii /home/dbermudez/Documents/subjects/00_0086/mri/orig/001.mgz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /home/dbermudez/Documents/subjects/RAW/00_0086/ns_00_0086_3T_T1w_MPR1.nii... TR=2456.67, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, 1) k_ras = (1, 0, 0) writing to /home/dbermudez/Documents/subjects/00_0086/mri/orig/001.mgz... @#@FSTIME 2019:11:13:13:43:32 mri_convert N 2 e 2.85 S 0.03 U 2.81 P 100% M 45928 F 0 R 10175 W 0 c 9 w 1 I 0 O 54616 L 0.29 0.35 0.35 @#@FSLOADPOST 2019:11:13:13:43:35 mri_convert N 2 0.35 0.36 0.36 /home/dbermudez/Documents/subjects/00_0086 mri_convert /home/dbermudez/Documents/subjects/RAW/00_0086/ns_00_0086_3T_T1w_MPR2.nii /home/dbermudez/Documents/subjects/00_0086/mri/orig/002.mgz mri_convert /home/dbermudez/Documents/subjects/RAW/00_0086/ns_00_0086_3T_T1w_MPR2.nii /home/dbermudez/Documents/subjects/00_0086/mri/orig/002.mgz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /home/dbermudez/Documents/subjects/RAW/00_0086/ns_00_0086_3T_T1w_MPR2.nii... TR=2456.67, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, 1) k_ras = (1, 0, 0) writing to /home/dbermudez/Documents/subjects/00_0086/mri/orig/002.mgz... @#@FSTIME 2019:11:13:13:43:35 mri_convert N 2 e 2.82 S 0.04 U 2.77 P 99% M 45996 F 0 R 10173 W 0 c 6 w 2 I 0 O 54672 L 0.35 0.36 0.36 @#@FSLOADPOST 2019:11:13:13:43:38 mri_convert N 2 0.40 0.37 0.36 lta_convert --src orig.mgz --trg /usr/local/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $ --src: orig.mgz src image (geometry). --trg: /usr/local/freesurfer/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. error: No such file or directory error: ltMNIreadEx: could not open file transforms/talairach.xfm error: mghRead(/home/dbermudez/Documents/subjects/00_0086/mri/orig.mgz, -1): could not open file ERROR readMNI: cannot read src MRIorig.mgz Linux dbermudez-XPS-15-9550 5.0.0-32-generic #34~18.04.2-Ubuntu SMP Thu Oct 10 10:36:02 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 00_0086 exited with ERRORS at Wed Nov 13 13:43:39 EST 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting