External Email - Use Caution
Hello Freesurfer Developpers,
I'm attempting to make a study specific template using all of my
subjects as input using the make_average_subject command, but am
receiving the following error:
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/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
Segmentation fault (core dumped)
Linux wbic-cs-5 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14)
x86_64 GNU/Linux
recon-all -s average_v2 exited with ERRORS at Fri Sep 21 11:11:25 BST
2018
I've attached here the full log file.
I read in this forum:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57030.html
to try installing the following patch:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
and had asked our computing support team to install it before the
current run of make_average_subject, so the error seems to be happening
despite the patch. I would greatly appreciate your suggestions for
resolving the error.
Thanks very much,
Colleen
Fri Sep 21 11:06:50 BST 2018
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2
/applications/freesurfer/freesurfer_6.0.0/bin/recon-all
-s average_v2 -cortribbon -aparc2aseg
subjid average_v2
setenv SUBJECTS_DIR /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0
Actual FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux wbic-cs-5 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize unlimited
coredumpsize unlimited
memoryuse 37748736 kbytes
vmemoryuse unlimited
descriptors 65536
memorylocked unlimited
maxproc 193538
maxlocks unlimited
maxsignal 193538
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 49564564 10631376 38933188 64716 177252 6734152
-/+ buffers/cache: 3719972 45844592
Swap: 16200696 133356 16067340
########################################
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: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 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: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 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: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:50-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 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: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 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: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/21-10:06:51-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: cper2 Machine: wbic-cs-5 Platform: Linux PlatformVersion: 3.16.0-6-amd64 CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /applications/freesurfer/freesurfer_6.0.0/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 /applications/freesurfer/freesurfer_6.0.0/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
#--------------------------------------------
#@# Cortical ribbon mask Fri Sep 21 11:06:51 BST 2018
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/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 average_v2
SUBJECTS_DIR is /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
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 = 1
writing volume /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/mri/ribbon.mgz
mris_volmask took 4.02 minutes
writing ribbon files
#-----------------------------------------
#@# AParc-to-ASeg aparc Fri Sep 21 11:10:52 BST 2018
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2
mri_aparc2aseg --s average_v2 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /applications/freesurfer/freesurfer_6.0.0/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: /applications/freesurfer/freesurfer_6.0.0/average/RB_all_2016-05-10.vc700.gca
label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
subject average_v2
outvol /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0
Reading lh white surface
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/surf/lh.white
Reading lh pial surface
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/surf/lh.pial
Loading lh annotations from /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/label/tmpdir.annot2std.23459/seg.1.Sub_001.ctab)
Reading rh white surface
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/surf/rh.white
Reading rh pial surface
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/surf/rh.pial
Loading rh annotations from /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/label/tmpdir.annot2std.15883/seg.1.Sub_001.ctab)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/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 /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/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
Segmentation fault (core dumped)
Linux wbic-cs-5 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64 GNU/Linux
recon-all -s average_v2 exited with ERRORS at Fri Sep 21 11:11:25 BST 2018
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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