Dear Freesurfer experts
Hi
I got an error when I was trying to make an average subject. I attached the log
file.
I appreciate if you could please let me know what the problem is.
make_average_subject --out avgsubject --subjects subj1 subj2 subj 3
labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from
Linux bee.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13
23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s avgsubject exited with ERRORS at Mon Feb 10 10:43:37 EST 2020
For more details, see the log file
/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thanks
Mona
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
Mon Feb 10 10:40:43 EST 2020
/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject
/usr/local/freesurfer/stable6/bin/recon-all
-s avgsubject -cortribbon -aparc2aseg
subjid avgsubject
setenv SUBJECTS_DIR /autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR
FREESURFER_HOME /usr/local/freesurfer/stable6
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6
build-stamp.txt: freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb
Linux bee.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize unlimited
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 65535
memorylocked 64 kbytes
maxproc 772023
maxlocks unlimited
maxsignal 772023
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 197833568 10569768 4984420 456692 182279380 186057864
Swap: 62499836 46848 62452988
########################################
program versions used
$Id: recon-all,v 1.580.2.15 2016/12/08 22:02:41 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info
ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:43-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
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: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
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: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/02/10-15:40:44-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:45-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:46-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
$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: 2020/02/10-15:40:46-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
$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: 2020/02/10-15:40:46-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:46-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:46-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:46-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:46-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/02/10-15:40:46-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800
#######################################
GCADIR /usr/local/freesurfer/stable6/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/stable6/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
#--------------------------------------------
#@# Cortical ribbon mask Mon Feb 10 10:40:46 EST 2020
/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/mri
mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon avgsubject
SUBJECTS_DIR is /autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR
loading input data...
computing distance to left white surface
computing distance to left pial surface
computing distance to right white surface
computing distance to right pial surface
hemi masks overlap voxels = 4
writing volume /autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/mri/ribbon.mgz
mris_volmask took 2.56 minutes
writing ribbon files
#-----------------------------------------
#@# AParc-to-ASeg aparc Mon Feb 10 10:43:20 EST 2020
/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject
mri_aparc2aseg --s avgsubject --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt
relabeling unlikely voxels interior to white matter surface:
norm: mri/norm.mgz
XFORM: mri/transforms/talairach.m3z
GCA: /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca
label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR
subject avgsubject
outvol /autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0
Reading lh white surface
/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/surf/lh.white
Reading lh pial surface
/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/surf/lh.pial
Loading lh annotations from /autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /scratch/tmpdir.annot2std.6411/seg.1.arap_7T_all.ctab)
Reading rh white surface
/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/surf/rh.white
Reading rh pial surface
/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/surf/rh.pial
Loading rh annotations from /autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /scratch/tmpdir.annot2std.9562/seg.1.arap_7T_all.ctab)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
mghRead(mri/norm.mgz, -1): could not open file
-------------------------
Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from
Linux bee.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s avgsubject exited with ERRORS at Mon Feb 10 10:43:37 EST 2020
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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