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Problem with lGI
by Avi Gharehgazlou 06 Sep '19

06 Sep '19

External Email - Use Caution Hi, I have ran the lGI flag many times in the past. However, now that I am trying to run the flag on a new group of participants I get the below error. Will you please tell me how I can fix this? Thanks so much, Avi New invocation of recon-all Fri Aug 30 16:47:49 EDT 2019 /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01 /usr/local/freesurfer/bin/recon-all -s MR160-114-0370_01 -localGI -openmp 2 subjid MR160-114-0370_01 setenv SUBJECTS_DIR /d/mjt/9/users/avideh/data/recon 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 apollo.sickkids.ca 4.15.0-50-generic #54-Ubuntu SMP Mon May 6 18:46:08 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 16384 kbytes maxproc 321903 maxlocks unlimited maxsignal 321903 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 82473464 18994140 26581924 374636 36897400 62364472 Swap: 8388604 1922560 6466044 ######################################## 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: 2019/08/30-20:47:49-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-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: 2019/08/30-20:47:49-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-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: 2019/08/30-20:47:49-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:49-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:49-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:49-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:49-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-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: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-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: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-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: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-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 ####################################### /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Aug 30 16:47:51 EDT 2019 mris_compute_lgi --i lh.pial ================= rm -Rf /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2019 The MathWorks, Inc. R2019a Update 4 (9.6.0.1150989) 64-bit (glnxa64) June 26, 2019 For online documentation, see https://www.mathworks.com/support For product information, visit www.mathworks.com. >> reading filled volume... closing volume... { Undefined variable "matlab" or class "matlab.graphics.chart.internal.datachk". Error in isosurface (line 76) data = matlab.graphics.chart.internal.datachk(data); Error in make_outer_surface (line 49) [f,v] = isosurface(BW2,100); } >> -------------------------------------------------------------------------------- std::terminate() detected at Fri Aug 30 16:48:20 2019 -0400 -------------------------------------------------------------------------------- Configuration: Crash Decoding : Disabled - No sandbox or build area path Crash Mode : continue (default) Default Encoding : US-ASCII Deployed : false Desktop Environment : MATE GNU C Library : 2.27 stable MATLAB Architecture : glnxa64 MATLAB Entitlement ID : 1261621 MATLAB Root : /usr/local/MATLAB/R2019a MATLAB Version : 9.6.0.1150989 (R2019a) Update 4 Operating System : Ubuntu 18.04.3 LTS Process ID : 2352 Processor ID : x86 Family 6 Model 44 Stepping 2, GenuineIntel Session Key : 75ad7f0e-24cf-4356-844c-9536f142fca0 Static TLS mitigation : Disabled: Unable to open display Window System : No active display Fault Count: 1 Abnormal termination: std::terminate() Register State (captured): RAX = 0000000000000000 RBX = 00007fee6ea82d98 RCX = 000000000000000a RDX = 00007fee6ea63e00 RSP = 00007fee4bff84a0 RBP = 00007fee4bff8860 RSI = 00007fee6ea2b3c6 RDI = 00007fee4bff84b0 R8 = 000000000000ffff R9 = 00007fee70e04740 R10 = 0000000000000000 R11 = 0000000000000005 R12 = 00007fee6ea72d08 R13 = 00007fee4bff8c20 R14 = 00007fee4bff9110 R15 = 00007fee4bff90e0 RIP = 00007fee6e97b1ae EFL = 00007fee6e8ab270 CS = 7480 FS = 71d8 GS = 7fee Stack Trace (captured): [ 0] 0x00007fee6e972713 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwfl.so+00829203 [ 1] 0x00007fee6e97290c /usr/local/MATLAB/R2019a/bin/glnxa64/libmwfl.so+00829708 _ZN10foundation4core4diag15stacktrace_base7captureEm+00000028 [ 2] 0x00007fee6e975052 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwfl.so+00839762 [ 3] 0x00007fee64201553 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01213779 [ 4] 0x00007fee64204157 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01225047 [ 5] 0x00007fee6420438a /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01225610 [ 6] 0x00007fee64204951 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01227089 [ 7] 0x00007fee642058d7 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01231063 [ 8] 0x00007fee70b1f3a6 /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00582566 [ 9] 0x00007fee70b1e3d9 /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00578521 [ 10] 0x00007fee70b1ed2d /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00580909 __gxx_personality_v0+00000717 [ 11] 0x00007fee70889f03 /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libgcc_s.so.1+00065283 [ 12] 0x00007fee7088a26b /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libgcc_s.so.1+00066155 _Unwind_RaiseException+00000251 [ 13] 0x00007fee70b1f5fb /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00583163 __cxa_throw+00000091 [ 14] 0x00007fee66376e22 /usr/local/MATLAB/R2019a/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoFoundation.so.48+00900642 _ZN4Poco10MemoryPool7releaseEPv+00000162 [ 15] 0x00007fee66966e5f /usr/local/MATLAB/R2019a/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoNet.so.48+00638559 _ZN4Poco3Net19HTTPHeaderStreamBufD2Ev+00000031 [ 16] 0x00007fee66967253 /usr/local/MATLAB/R2019a/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoNet.so.48+00639571 _ZN4Poco3Net21HTTPHeaderInputStreamD1Ev+00000067 [ 17] 0x00007fee6695abc7 /usr/local/MATLAB/R2019a/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoNet.so.48+00588743 _ZN4Poco3Net17HTTPClientSession15receiveResponseERNS0_12HTTPResponseE+00000199 [ 18] 0x00007fee58a7c827 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/../../../../bin/glnxa64/libmwflhttpclient.so+00141351 [ 19] 0x00007fee58a76d38 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/../../../../bin/glnxa64/libmwflhttpclient.so+00118072 [ 20] 0x00007fee58a7117d /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/../../../../bin/glnxa64/libmwflhttpclient.so+00094589 _ZNK10foundation10httpclient16WebServiceClient23doWebServiceTransactionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS8_S8_St4lessIS8_ESaISt4pairIS8_S8_EEES9_RNS1_18WebServiceResponseEiS9_+00000061 [ 21] 0x00007fee58a72409 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/../../../../bin/glnxa64/libmwflhttpclient.so+00099337 _ZNK10foundation10httpclient16WebServiceClient25makeWebServiceTransactionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS8_S8_St4lessIS8_ESaISt4pairIS8_S8_EEES9_RNS1_18WebServiceResponseEiiS9_+00000121 [ 22] 0x00007fee58c02387 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00590727 [ 23] 0x00007fee58c0675b /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00608091 [ 24] 0x00007fee58be9a68 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00490088 [ 25] 0x00007fee58c6beaa /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+01023658 [ 26] 0x00007fee58bf090a /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00518410 [ 27] 0x00007fee6ef5f7ad /usr/local/MATLAB/R2019a/bin/glnxa64/libmwms.so+02697133 [ 28] 0x00007fee58bf0586 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00517510 [ 29] 0x00007fee6fe54bdd /usr/local/MATLAB/R2019a/bin/glnxa64/libmwboost_thread.so.1.65.1+00080861 [ 30] 0x00007fee70e196db /lib/x86_64-linux-gnu/libpthread.so.0+00030427 [ 31] 0x00007fee705aa88f /lib/x86_64-linux-gnu/libc.so.6+01185935 clone+00000063 [ 32] 0x0000000000000000 <unknown-module>+00000000 ** This crash report has been saved to disk as /home/avideh/matlab_crash_dump.2352-1 ** MATLAB is exiting because of fatal error Killed ERROR: make_outer_surface did not create output file '/d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux apollo.sickkids.ca 4.15.0-50-generic #54-Ubuntu SMP Mon May 6 18:46:08 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MR160-114-0370_01 exited with ERRORS at Fri Aug 30 16:48:21 EDT 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 1

(revised) mri_glmfit error
by Gwang-Won Kim 06 Sep '19

06 Sep '19

1 0

Using mask image
by Gwang-Won Kim 05 Sep '19

05 Sep '19

2 1

How to generate a solid volume from lh/rh.pial-outer-smoothed
by Jingya Miao 05 Sep '19

05 Sep '19

External Email - Use Caution Hello Freesurfer Developers, I am trying to generate a solid volume out of the lh/rh.pial-outer-smoothed file. I was able to get just the surface in .nii format by using: mri_surf2vol --hemi lh --surf pial-outer-smoothed --mkmask --reg mri/register.dat --o surfsmoothed.nii --template mri/T1.nii --subject BerA I also attempted to use --fillribbon mri_surf2vol --surfval $SUBJECTS_DIR/Berger_Andrew/surf/lh.pial-outer-smoothed --fillribbon --reg mri/register.dat --o smoothedfill.nii --template T1.nii --subject BerA gdiagno = -1 ERROR: cannot recognize the type of /Users/mah.ali/freesurfer/subjects/Ber A/surf/lh.pial-outer-smoothed I am wondering what would be a good way to generate a solid volume out of the pill-outer-smoothed files. Thank you, Miao

2 1

Interruption during data processing
by Троицкий Антон Александрович 05 Sep '19

05 Sep '19

External Email - Use Caution Dear freesurfer users, I encountered a problem when data processing suddenly interrupted. Is there any way to continue procession of patient data and don't repeat previous steps and don't waste the time? Best regards, Anton Troitskii.

2 1

Re: [Freesurfer] Problem with lazy symbol binding failed
by fsbuild 05 Sep '19

05 Sep '19

External Email - Use Caution Hello Minsun, You can try downloading this link to a zip file with an updated version of 6.0.0 freeview for the Mac.  Follow the instructions in README.patch.https://drive.google.com/file/d/1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh… R. On Sep 5, 2019, at 02:56, Minsun Park <vd.mpark(a)gmail.com> wrote:        External Email - Use Caution        HiI've tried to run @SUMA_Make_Spec_FS in afni but I've kept getting this error message (which is written at the end of this email).I'm using Mac (high sierra 10.13.6), the latest afni, XQuartz(2.10.11).Using Freesurfer I made a flattened map by running recon-all and tksurfer without any problems.I disabled SIPs and updated Freesurfer (as recommended in this link: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-April…'d appreciate if you give any suggestions I can do!######bash-3.2$ @SUMA_Make_Spec_FS -fspath ../ -NIFTI -sid 060717KHW++ creating directory './SUMA' for results...-- found 8 LH surfaces-- found 8 RH surfacesmri_convert.bin -ot nii /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/mri/orig.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/orig.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/mri/orig.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/orig.nii...++ created AFNI file './SUMA/060717KHW_SurfVol.nii'Made roi label table for AFNI - fs_table.niml.ltmri_convert.bin -ot nii mri/T1.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/T1.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/T1.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/T1.nii...mri_convert.bin -ot nii mri/aparc+aseg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc+aseg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/aparc+aseg.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc+aseg.nii...++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]++ Authored by: RW Cox** AFNI converts NIFTI_datatype=8 (INT32) in file aparc+aseg.nii to FLOAT32     Warnings of this type will be muted for this session.     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.++ Processing AFNI dataset aparc+aseg.nii + setting labeltable + loading and re-writing dataset aparc+aseg.nii (./aparc+aseg.nii in NIFTI storage)++ 3drefit processed 1 datasetsProgram 3dmerge ++ 3dmerge: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]3dmerge: edit and combine 3D datasets, by RW Cox++ default -1dindex = 0++ default -1tindex = 1++ editing input dataset in memory (64.0 MB).-- Wrote edited dataset: ./aparc+aseg_rank.nii++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]++ Authored by: RW Cox++ Processing AFNI dataset aparc+aseg_rank.nii + setting labeltable + loading and re-writing dataset aparc+aseg_rank.nii (./aparc+aseg_rank.nii in NIFTI storage)++ 3drefit processed 1 datasetsNotice: SessionAtlases.niml already exists, appending to it aparc+aseg_rank.mri_convert.bin -ot nii mri/aparc.a2009s+aseg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc.a2009s+aseg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/aparc.a2009s+aseg.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc.a2009s+aseg.nii...++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]++ Authored by: RW Cox** AFNI converts NIFTI_datatype=8 (INT32) in file aparc.a2009s+aseg.nii to FLOAT32     Warnings of this type will be muted for this session.     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.++ Processing AFNI dataset aparc.a2009s+aseg.nii + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg.nii (./aparc.a2009s+aseg.nii in NIFTI storage)++ 3drefit processed 1 datasetsNotice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg.Program 3dmerge ++ 3dmerge: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]3dmerge: edit and combine 3D datasets, by RW Cox++ default -1dindex = 0++ default -1tindex = 1++ editing input dataset in memory (64.0 MB).-- Wrote edited dataset: ./aparc.a2009s+aseg_rank.nii++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]++ Authored by: RW Cox++ Processing AFNI dataset aparc.a2009s+aseg_rank.nii + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg_rank.nii (./aparc.a2009s+aseg_rank.nii in NIFTI storage)++ 3drefit processed 1 datasetsNotice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg_rank.mri_convert.bin -ot nii mri/aseg.auto.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.auto.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/aseg.auto.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.auto.nii...mri_convert.bin -ot nii mri/aseg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/aseg.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.nii...++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]++ Authored by: RW Cox** AFNI converts NIFTI_datatype=8 (INT32) in file aseg..nii to FLOAT32     Warnings of this type will be muted for this session.     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.++ Processing AFNI dataset aseg.nii + setting labeltable + loading and re-writing dataset aseg.nii (./aseg.nii in NIFTI storage)++ 3drefit processed 1 datasetsNotice: SessionAtlases.niml already exists, appending to it aseg.Program 3dmerge ++ 3dmerge: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]3dmerge: edit and combine 3D datasets, by RW Cox++ default -1dindex = 0++ default -1tindex = 1++ editing input dataset in memory (64.0 MB).-- Wrote edited dataset: ./aseg_rank.nii++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit]++ Authored by: RW Cox++ Processing AFNI dataset aseg_rank.nii + setting labeltable + loading and re-writing dataset aseg_rank.nii (./aseg_rank.nii in NIFTI storage)++ 3drefit processed 1 datasetsNotice: SessionAtlases.niml already exists, appending to it aseg_rank.mri_convert.bin -ot nii mri/brain.finalsurfs.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.finalsurfs.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/brain.finalsurfs.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.finalsurfs.nii...mri_convert.bin -ot nii mri/brain.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/brain.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.nii...mri_convert.bin -ot nii mri/brainmask.auto.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.auto.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/brainmask.auto.mgz...TR=2300.00, TE=2..28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.auto.nii...mri_convert.bin -ot nii mri/brainmask.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/brainmask.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.nii...mri_convert.bin -ot nii mri/norm.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/norm.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/norm.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/norm.nii...mri_convert.bin -ot nii mri/nu.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/nu.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/nu.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/nu.nii...mri_convert.bin -ot nii mri/lh.ribbon.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/lh.ribbon.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/lh.ribbon.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/lh.ribbon.nii...mri_convert.bin -ot nii mri/rh.ribbon.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/rh.ribbon.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/rh.ribbon.mgz....TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/rh.ribbon.nii...mri_convert.bin -ot nii mri/wm.asegedit.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.asegedit.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/wm.asegedit.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.asegedit.nii...mri_convert.bin -ot nii mri/wm.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/wm.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.nii...mri_convert.bin -ot nii mri/wm.seg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.seg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from mri/wm.seg.mgz...TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00i_ras = (-1, 9.31323e-10, 0)j_ras = (9.31323e-10, -1.45519e-11, -1)k_ras = (0, 1, 7.27596e-12)writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.seg.nii...-- running 'mris_convert lh.smoothwm lh.smoothwm.asc'Abortdyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibdyld: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibdyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibdyld: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibAbortc_ras: Subscript out of range.c_ras: Subscript out of range.Thanks,Minsun_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Problem with lazy symbol binding failed
by Minsun Park 05 Sep '19

05 Sep '19

External Email - Use Caution Hi I've tried to run @SUMA_Make_Spec_FS in afni but I've kept getting this error message (which is written at the end of this email). I'm using Mac (high sierra 10.13.6), the latest afni, XQuartz(2.10.11). Using Freesurfer I made a flattened map by running recon-all and tksurfer without any problems. I disabled SIPs and updated Freesurfer (as recommended in this link: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-April/061591.html ). I'd appreciate if you give any suggestions I can do! ###### bash-3.2$ @SUMA_Make_Spec_FS -fspath ./ -NIFTI -sid 060717KHW ++ creating directory './SUMA' for results... -- found 8 LH surfaces -- found 8 RH surfaces mri_convert.bin -ot nii /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/mri/orig.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/orig.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/mri/orig.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/orig.nii... ++ created AFNI file './SUMA/060717KHW_SurfVol.nii' Made roi label table for AFNI - fs_table.niml.lt mri_convert.bin -ot nii mri/T1.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/T1.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/T1.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/T1.nii... mri_convert.bin -ot nii mri/aparc+aseg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc+aseg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/aparc+aseg.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc+aseg.nii... ++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] ++ Authored by: RW Cox ** AFNI converts NIFTI_datatype=8 (INT32) in file aparc+aseg.nii to FLOAT32 Warnings of this type will be muted for this session. Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none. ++ Processing AFNI dataset aparc+aseg.nii + setting labeltable + loading and re-writing dataset aparc+aseg.nii (./aparc+aseg.nii in NIFTI storage) ++ 3drefit processed 1 datasets Program 3dmerge ++ 3dmerge: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] 3dmerge: edit and combine 3D datasets, by RW Cox ++ default -1dindex = 0 ++ default -1tindex = 1 ++ editing input dataset in memory (64.0 MB) . -- Wrote edited dataset: ./aparc+aseg_rank.nii ++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc+aseg_rank.nii + setting labeltable + loading and re-writing dataset aparc+aseg_rank.nii (./aparc+aseg_rank.nii in NIFTI storage) ++ 3drefit processed 1 datasets Notice: SessionAtlases.niml already exists, appending to it aparc+aseg_rank. mri_convert.bin -ot nii mri/aparc.a2009s+aseg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc.a2009s+aseg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/aparc.a2009s+aseg.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aparc.a2009s+aseg.nii... ++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] ++ Authored by: RW Cox ** AFNI converts NIFTI_datatype=8 (INT32) in file aparc.a2009s+aseg.nii to FLOAT32 Warnings of this type will be muted for this session. Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none. ++ Processing AFNI dataset aparc.a2009s+aseg.nii + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg.nii (./aparc.a2009s+aseg.nii in NIFTI storage) ++ 3drefit processed 1 datasets Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg. Program 3dmerge ++ 3dmerge: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] 3dmerge: edit and combine 3D datasets, by RW Cox ++ default -1dindex = 0 ++ default -1tindex = 1 ++ editing input dataset in memory (64.0 MB) . -- Wrote edited dataset: ./aparc.a2009s+aseg_rank.nii ++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc.a2009s+aseg_rank.nii + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg_rank.nii (./aparc.a2009s+aseg_rank.nii in NIFTI storage) ++ 3drefit processed 1 datasets Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg_rank. mri_convert.bin -ot nii mri/aseg.auto.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.auto.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/aseg.auto.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.auto.nii... mri_convert.bin -ot nii mri/aseg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/aseg.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/aseg.nii... ++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] ++ Authored by: RW Cox ** AFNI converts NIFTI_datatype=8 (INT32) in file aseg.nii to FLOAT32 Warnings of this type will be muted for this session. Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none. ++ Processing AFNI dataset aseg.nii + setting labeltable + loading and re-writing dataset aseg.nii (./aseg.nii in NIFTI storage) ++ 3drefit processed 1 datasets Notice: SessionAtlases.niml already exists, appending to it aseg. Program 3dmerge ++ 3dmerge: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] 3dmerge: edit and combine 3D datasets, by RW Cox ++ default -1dindex = 0 ++ default -1tindex = 1 ++ editing input dataset in memory (64.0 MB) . -- Wrote edited dataset: ./aseg_rank.nii ++ 3drefit: AFNI version=AFNI_19.2.21 (Aug 29 2019) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aseg_rank.nii + setting labeltable + loading and re-writing dataset aseg_rank.nii (./aseg_rank.nii in NIFTI storage) ++ 3drefit processed 1 datasets Notice: SessionAtlases.niml already exists, appending to it aseg_rank. mri_convert.bin -ot nii mri/brain.finalsurfs.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.finalsurfs.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/brain.finalsurfs.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.finalsurfs.nii... mri_convert.bin -ot nii mri/brain.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/brain.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brain.nii... mri_convert.bin -ot nii mri/brainmask.auto.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.auto.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/brainmask.auto.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.auto.nii... mri_convert.bin -ot nii mri/brainmask.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/brainmask.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/brainmask.nii... mri_convert.bin -ot nii mri/norm.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/norm.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/norm.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/norm.nii... mri_convert.bin -ot nii mri/nu.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/nu.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/nu.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/nu.nii... mri_convert.bin -ot nii mri/lh.ribbon.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/lh.ribbon.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/lh.ribbon.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/lh.ribbon.nii... mri_convert.bin -ot nii mri/rh.ribbon.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/rh.ribbon.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/rh.ribbon.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/rh.ribbon.nii... mri_convert.bin -ot nii mri/wm.asegedit.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.asegedit.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/wm.asegedit.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.asegedit.nii... mri_convert.bin -ot nii mri/wm.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/wm.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.nii... mri_convert.bin -ot nii mri/wm.seg.mgz /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.seg.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from mri/wm.seg.mgz... TR=2300.00, TE=2.28, TI=900.00, flip angle=8.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (9.31323e-10, -1.45519e-11, -1) k_ras = (0, 1, 7.27596e-12) writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/RetResult/./SUMA/wm.seg.nii... -- running 'mris_convert lh.smoothwm lh.smoothwm.asc' Abort dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Abort c_ras: Subscript out of range. c_ras: Subscript out of range. Thanks, Minsun

1 0

Re: [Freesurfer] Invaild Key Error for Freesurfer 5.1
by fsbuild 04 Sep '19

04 Sep '19

External Email - Use Caution Hello An, Try taking the attached file “license_5” and rename it to “.license”   Then put it under $FREESURFER_HOME so that you see it when you issue the command, $ ls $FREESURFER_HOME/.license - R. On Sep 4, 2019, at 22:50, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello An,My understanding is that in Freesurfer 5 you need to have a file called “.license” and it should be placed in the directory where you installed freesurfer.  That directory is also the path the variable $FREESURFER_HOME points to.So if there was no “.license” file there to begin with, then this command would have reported there was no such file,$ ls  $FRESSURFER_HOME/.licenseNewer versions of Freesurfer look for “license.txt”.   Did you rename the newly generated “license.txt” file and copy it to live under $FREESURFER_HOME to be “.license” ?, e..g., from wherever “license.txt” maybe you did something like,$ cp license.txt  $FREESURFER_HOME/.licenseI was going to suggest you try doing that copy to create what freesurfer 5 is looking for, but from your output below, it looks like you already did that and it is finding $FREESURFER_HOME/.license but saying the key is incorrect to run version 5..I don’t know how to change/re-generate a key to work with version 5, but we can look into it.    - R.On Sep 4, 2019, at 20:56, An Lijun <lijun.an(a)hotmail.com> wrote:        External Email - Use Caution        Dear Freesurfer experts,Right now I am trying to use Freesurfer 5.1.0. But the software showed ERROR “Invalid FreeSurfer license key found in license file”. We tried to apply license online, however, the license provided online is now for 6.0.0 version and it seems not applicable for 5.1.0 since I still got the same error message as before..May I ask how to get the licnese of 5.1.0?The tricky part is the format of lecense now I get from Fresssurfer is different from the old one in Freesurfer 5.1.New License I get(call license.txt):xxxxxxxx@gmail.com43508 *CRBDdLNbgmws FSOkaDD5AxOQkOld License(call .license):xxxxxxxx@gmail.com39689*1PS: I tried to use `dos2unix` to transfer the license to unix format, but it seems no help. Thanks for your help! ------------------------------------------------------------------------------------------------------------------------------------------Best Regards,An Lijun_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] Invaild Key Error for Freesurfer 5.1
by fsbuild 04 Sep '19

04 Sep '19

External Email - Use Caution Hello An, My understanding is that in Freesurfer 5 you need to have a file called “.license” and it should be placed in the directory where you installed freesurfer.  That directory is also the path the variable $FREESURFER_HOME points to. So if there was no “.license” file there to begin with, then this command would have reported there was no such file, $ ls  $FRESSURFER_HOME/.license Newer versions of Freesurfer look for “license.txt”.   Did you rename the newly generated “license.txt” file and copy it to live under $FREESURFER_HOME to be “.license” ?, e.g., from wherever “license.txt” maybe you did something like, $ cp license.txt  $FREESURFER_HOME/.license I was going to suggest you try doing that copy to create what freesurfer 5 is looking for, but from your output below, it looks like you already did that and it is finding $FREESURFER_HOME/.license but saying the key is incorrect to run version 5. I don’t know how to change/re-generate a key to work with version 5, but we can look into it.     - R. On Sep 4, 2019, at 20:56, An Lijun <lijun.an(a)hotmail.com> wrote:        External Email - Use Caution        Dear Freesurfer experts,Right now I am trying to use Freesurfer 5.1.0. But the software showed ERROR “Invalid FreeSurfer license key found in license file”. We tried to apply license online, however, the license provided online is now for 6.0.0 version and it seems not applicable for 5.1.0 since I still got the same error message as before.May I ask how to get the licnese of 5.1.0?The tricky part is the format of lecense now I get from Fresssurfer is different from the old one in Freesurfer 5.1.New License I get(call license.txt):xxxxxxxx@gmail.com43508 *CRBDdLNbgmws FSOkaDD5AxOQkOld License(call .license):xxxxxxxx@gmail.com39689*1PS: I tried to use `dos2unix` to transfer the license to unix format, but it seems no help. Thanks for your help! ------------------------------------------------------------------------------------------------------------------------------------------Best Regards,An Lijun_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Invaild Key Error for Freesurfer 5.1
by An Lijun 04 Sep '19

04 Sep '19

External Email - Use Caution Dear Freesurfer experts, Right now I am trying to use Freesurfer 5.1.0. But the software showed ERROR “Invalid FreeSurfer license key found in license file”. We tried to apply license online, however, the license provided online is now for 6.0.0 version and it seems not applicable for 5.1.0 since I still got the same error message as before. May I ask how to get the licnese of 5.1.0? The tricky part is the format of lecense now I get from Fresssurfer is different from the old one in Freesurfer 5.1. New License I get(call license.txt): xxxxxxxx(a)gmail.com<mailto:xxxxxxxx@gmail.com> 43508 *CRBDdLNbgmws FSOkaDD5AxOQk Old License(call .license): xxxxxxxx(a)gmail.com<mailto:xxxxxxxx@gmail.com> 39689 *1 PS: I tried to use `dos2unix` to transfer the license to unix format, but it seems no help. Thanks for your help! ------------------------------------------------------------------------------------------------------------------------------------------ Best Regards, An Lijun

1 0

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