vr 9 mrt 2018 13:41:51 CET /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon /usr/local/freesurfer/bin/recon-all -i sub-CC00172BN08_fakeT1.nii -subject asub-CC00172BN08_recon subjid asub-CC00172BN08_recon setenv SUBJECTS_DIR /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1 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 theresa-Lenovo-IdeaPad 4.13.0-36-generic #40~16.04.1-Ubuntu SMP Fri Feb 16 23:25:58 UTC 2018 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 31045 maxlocks unlimited maxsignal 31045 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 8066704 2918852 2164836 354004 2983016 4428552 Swap: 8287228 421996 7865232 ######################################## 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: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:51-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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 ####################################### /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon mri_convert /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/sub-CC00172BN08_fakeT1.nii /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/orig/001.mgz mri_convert.bin /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/sub-CC00172BN08_fakeT1.nii /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/orig/001.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/sub-CC00172BN08_fakeT1.nii... TR=1.00, 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/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/orig/001.mgz... Started at vr 9 mrt 2018 13:41:51 CET Ended at vr 9 mrt 2018 13:41:54 CET #@#%# recon-all-run-time-hours 0,001 recon-all -s asub-CC00172BN08_recon finished without error at vr 9 mrt 2018 13:41:54 CET New invocation of recon-all vr 9 mrt 2018 13:41:55 CET /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon /usr/local/freesurfer/bin/recon-all -autorecon1 -noskullstrip -notal-check -s asub-CC00172BN08_recon subjid asub-CC00172BN08_recon setenv SUBJECTS_DIR /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1 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 theresa-Lenovo-IdeaPad 4.13.0-36-generic #40~16.04.1-Ubuntu SMP Fri Feb 16 23:25:58 UTC 2018 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 31045 maxlocks unlimited maxsignal 31045 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 8066704 2918904 1893840 350916 3253960 4431652 Swap: 8287228 421996 7865232 ######################################## 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: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:41:55-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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 ####################################### #-------------------------------------------- #@# MotionCor vr 9 mrt 2018 13:41:55 CET Found 1 runs /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/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/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/orig/001.mgz /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/rawavg.mgz /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon mri_convert /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/rawavg.mgz /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/orig.mgz --conform mri_convert.bin /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/rawavg.mgz /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/rawavg.mgz... TR=1.00, 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/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/orig.mgz... mri_add_xform_to_header -c /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/transforms/talairach.xfm /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/orig.mgz /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach vr 9 mrt 2018 13:42:03 CET /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/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 theresa-Lenovo-IdeaPad 4.13.0-36-generic #40~16.04.1-Ubuntu SMP Fri Feb 16 23:25:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux vr 9 mrt 2018 13:42:03 CET 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.6221 /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6221/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.6221/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1.00, 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.6221/nu0.mnc... -------------------------------------------------------- Iteration 1 vr 9 mrt 2018 13:42:05 CET nu_correct -clobber ./tmp.mri_nu_correct.mni.6221/nu0.mnc ./tmp.mri_nu_correct.mni.6221/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.6221/0/ -iterations 1000 -distance 50 [theresa@theresa-Lenovo-IdeaPad:/media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/] [2018-03-09 13:42:05] 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.6221/0/ ./tmp.mri_nu_correct.mni.6221/nu0.mnc ./tmp.mri_nu_correct.mni.6221/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 3 CV of field change: 0.000484714 mri_convert ./tmp.mri_nu_correct.mni.6221/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.6221/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.6221/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... vr 9 mrt 2018 13:42:37 CET 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 vr 9 mrt 2018 13:42:37 CET Ended at vr 9 mrt 2018 13:43:15 CET talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Nu Intensity Correction vr 9 mrt 2018 13:43:17 CET mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/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 theresa-Lenovo-IdeaPad 4.13.0-36-generic #40~16.04.1-Ubuntu SMP Fri Feb 16 23:25:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux vr 9 mrt 2018 13:43:17 CET 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.6483 /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6483/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.6483/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1.00, 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.6483/nu0.mnc... -------------------------------------------------------- Iteration 1 vr 9 mrt 2018 13:43:19 CET nu_correct -clobber ./tmp.mri_nu_correct.mni.6483/nu0.mnc ./tmp.mri_nu_correct.mni.6483/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.6483/0/ [theresa@theresa-Lenovo-IdeaPad:/media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/] [2018-03-09 13:43:19] 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.6483/0/ ./tmp.mri_nu_correct.mni.6483/nu0.mnc ./tmp.mri_nu_correct.mni.6483/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 2 CV of field change: 0.000716364 -------------------------------------------------------- Iteration 2 vr 9 mrt 2018 13:43:45 CET nu_correct -clobber ./tmp.mri_nu_correct.mni.6483/nu1.mnc ./tmp.mri_nu_correct.mni.6483/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.6483/1/ [theresa@theresa-Lenovo-IdeaPad:/media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/] [2018-03-09 13:43:45] 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.6483/1/ ./tmp.mri_nu_correct.mni.6483/nu1.mnc ./tmp.mri_nu_correct.mni.6483/nu2.imp Processing:.................................................................Done Number of iterations: 1 CV of field change: 0.000462992 mri_binarize --i ./tmp.mri_nu_correct.mni.6483/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.6483/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.6483/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.6483/ones.mgz sysname Linux hostname theresa-Lenovo-IdeaPad machine x86_64 user theresa input ./tmp.mri_nu_correct.mni.6483/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.6483/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.6483/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6483/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6483/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.6483/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6483/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6483/input.mean.dat sysname Linux hostname theresa-Lenovo-IdeaPad machine x86_64 user theresa UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6483/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.6483/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6483/ones.mgz --i ./tmp.mri_nu_correct.mni.6483/nu2.mnc --sum ./tmp.mri_nu_correct.mni.6483/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6483/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.6483/ones.mgz --i ./tmp.mri_nu_correct.mni.6483/nu2.mnc --sum ./tmp.mri_nu_correct.mni.6483/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6483/output.mean.dat sysname Linux hostname theresa-Lenovo-IdeaPad machine x86_64 user theresa UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6483/ones.mgz Loading ./tmp.mri_nu_correct.mni.6483/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.6483/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.6483/nu2.mnc ./tmp.mri_nu_correct.mni.6483/nu2.mnc mul .99926842013586483191 Saving result to './tmp.mri_nu_correct.mni.6483/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.6483/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.6483/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.6483/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 type change took 0 minutes and 8 seconds. mapping ( 0, 250) to ( 3, 110) vr 9 mrt 2018 13:44:38 CET mri_nu_correct.mni done mri_add_xform_to_header -c /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization vr 9 mrt 2018 13:44:39 CET /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/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 7.56427 74.25940 -50.11151 -357.42480; 1452.33386 21370.72852 -14403.94824 -109821.50000; -377.78531 -5569.93799 3741.47900 29094.62500; 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 = 4 Starting OpenSpline(): npoints = 4 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 111 gm peak at 76 (73), valley at 64 (61) csf peak at 37, setting threshold to 63 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 57 (54), valley at 45 (42) csf peak at 33, setting threshold to 49 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 48 seconds. Started at vr 9 mrt 2018 13:41:55 CET Ended at vr 9 mrt 2018 13:46:27 CET #@#%# recon-all-run-time-hours 0,076 recon-all -s asub-CC00172BN08_recon finished without error at vr 9 mrt 2018 13:46:27 CET New invocation of recon-all vr 9 mrt 2018 13:46:28 CET /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon /usr/local/freesurfer/bin/recon-all -autorecon2 -autorecon3 -s asub-CC00172BN08_recon subjid asub-CC00172BN08_recon setenv SUBJECTS_DIR /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1 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 theresa-Lenovo-IdeaPad 4.13.0-36-generic #40~16.04.1-Ubuntu SMP Fri Feb 16 23:25:58 UTC 2018 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 31045 maxlocks unlimited maxsignal 31045 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 8066704 2984996 938108 342544 4143600 4373564 Swap: 8287228 421996 7865232 ######################################## 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: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/09-12:46:28-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: theresa Machine: theresa-Lenovo-IdeaPad Platform: Linux PlatformVersion: 4.13.0-36-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 ####################################### #------------------------------------- #@# EM Registration vr 9 mrt 2018 13:46:28 CET /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/mri mri_em_register -rusage /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/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 setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register 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=12.0 skull bounding box = (86, 92, 74) --> (170, 178, 170) using (114, 121, 122) as brain centroid... mean wm in atlas = 107, using box (104,111,110) --> (124, 131,133) to find MRI wm before smoothing, mri peak at 113 robust fit to distribution - 83 +- 2.1 after smoothing, mri peak at 113, scaling input intensities by 0.947 scaling channel 0 by 0.946903 initial log_p = -4.638 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.532279 @ (9.091, -27.273, -27.273) max log p = -4.511023 @ (13.636, 13.636, 13.636) max log p = -4.495766 @ (-15.909, -15.909, -15.909) max log p = -4.473578 @ (-7.955, -1.136, -1.136) max log p = -4.472440 @ (0.568, -0.568, -1.705) max log p = -4.472440 @ (0.000, 0.000, 0.000) Found translation: (-0.6, -31.3, -32.4): log p = -4.472 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.232, old_max_log_p =-4.472 (thresh=-4.5) 1.22567 0.04176 -0.15586 -14.64658; 0.00000 1.19413 0.31997 -81.49915; 0.16136 -0.31723 1.18391 -18.88396; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.710, old_max_log_p =-4.232 (thresh=-4.2) 1.51833 0.13294 0.11291 -99.09834; -0.16778 1.38362 0.62705 -115.51429; -0.04768 -0.63535 1.38917 27.13906; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.399, old_max_log_p =-3.710 (thresh=-3.7) 1.74608 0.15288 0.12985 -132.97365; -0.19895 1.78501 0.57364 -150.01599; -0.07789 -0.45390 1.58177 -15.90242; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.397, old_max_log_p =-3.399 (thresh=-3.4) 1.75238 -0.02397 -0.15194 -77.69404; 0.03004 1.79726 0.55859 -179.25369; 0.15069 -0.43006 1.58518 -48.76333; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.270, old_max_log_p =-3.397 (thresh=-3.4) 1.69220 0.03852 -0.00208 -95.76566; -0.07087 1.74743 0.71108 -176.40347; 0.02578 -0.62603 1.58596 -4.17130; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.269, old_max_log_p =-3.270 (thresh=-3.3) 1.69220 0.03852 -0.00208 -95.76566; -0.06999 1.72601 0.76259 -179.83167; 0.02756 -0.67006 1.53256 7.43500; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.241, old_max_log_p =-3.269 (thresh=-3.3) 1.69418 0.03857 -0.00208 -96.02580; -0.07068 1.74285 0.74001 -180.17323; 0.02647 -0.64323 1.54846 1.37532; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.238, old_max_log_p =-3.241 (thresh=-3.2) 1.69418 0.03857 -0.00208 -96.02580; -0.07060 1.74080 0.73914 -179.82146; 0.02654 -0.64474 1.55209 1.13140; 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 1.69418 0.03857 -0.00208 -96.02580; -0.07060 1.74080 0.73914 -179.82146; 0.02654 -0.64474 1.55209 1.13140; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.69418 0.03857 -0.00208 -96.02580; -0.07060 1.74080 0.73914 -179.82146; 0.02654 -0.64474 1.55209 1.13140; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.69418 0.03857 -0.00208 -96.02580; -0.07060 1.74080 0.73914 -179.82146; 0.02654 -0.64474 1.55209 1.13140; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.238 (old=-4.638) transform before final EM align: 1.69418 0.03857 -0.00208 -96.02580; -0.07060 1.74080 0.73914 -179.82146; 0.02654 -0.64474 1.55209 1.13140; 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 1.69418 0.03857 -0.00208 -96.02580; -0.07060 1.74080 0.73914 -179.82146; 0.02654 -0.64474 1.55209 1.13140; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.69418 0.03857 -0.00208 -96.02580; -0.07060 1.74080 0.73914 -179.82146; 0.02654 -0.64474 1.55209 1.13140; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 011: -log(p) = 3.8 after pass:transform: ( 1.70, 0.04, -0.00, -96.03) ( -0.07, 1.74, 0.74, -179.82) ( 0.03, -0.64, 1.55, 1.13) dfp_em_step_func: 012: -log(p) = 3.8 after pass:transform: ( 1.70, 0.04, -0.00, -96.03) ( -0.07, 1.74, 0.74, -179.82) ( 0.03, -0.64, 1.55, 1.13) dfp_em_step_func: 013: -log(p) = 3.8 after pass:transform: ( 1.70, 0.04, -0.00, -96.03) ( -0.07, 1.74, 0.74, -179.82) ( 0.03, -0.64, 1.55, 1.13) dfp_em_step_func: 014: -log(p) = 3.8 after pass:transform: ( 1.70, 0.04, -0.00, -96.03) ( -0.07, 1.74, 0.74, -179.82) ( 0.03, -0.64, 1.55, 1.13) pass 2 through quasi-newton minimization... outof QuasiNewtonEMA: 016: -log(p) = 3.8 tol 0.000000 final transform: 1.69635 0.04086 -0.00003 -96.02580; -0.07012 1.74107 0.73971 -179.82146; 0.02885 -0.64219 1.55387 1.13140; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 754.949538 mri_em_register stimesec 1.676012 mri_em_register ru_maxrss 603112 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 162495 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 308 mri_em_register ru_nivcsw 2574 registration took 12 minutes and 37 seconds. #-------------------------------------- #@# CA Normalize vr 9 mrt 2018 13:59:05 CET /media/theresa/Seagate/dhcp_rel_1.1/derivatives/asub-CC00172BN08/ses-57300/anat/T1/asub-CC00172BN08_recon/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=6.0 skull bounding box = (85, 90, 72) --> (170, 179, 172) using (113, 120, 122) as brain centroid... mean wm in atlas = 107, using box (103,109,110) --> (123, 130,134) to find MRI wm before smoothing, mri peak at 113 robust fit to distribution - 113 +- 1.9 after smoothing, mri peak at 113, scaling input intensities by 0.947 scaling channel 0 by 0.946903 using 246344 sample points... INFO: compute sample coordinates transform 1.69635 0.04086 -0.00003 -96.02580; -0.07012 1.74107 0.73971 -179.82146; 0.02885 -0.64219 1.55387 1.13140; 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 (127, 91, 74) --> (167, 160, 169) Abort (core dumped) Linux theresa-Lenovo-IdeaPad 4.13.0-36-generic #40~16.04.1-Ubuntu SMP Fri Feb 16 23:25:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s asub-CC00172BN08_recon exited with ERRORS at vr 9 mrt 2018 13:59:19 CET To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting