I don't know what is going on there except that the average surfaces are probably wrong in some way. It looks like it made it all the way through except for that step, so all of the output should be there. How does it look?
On 03/13/2018 05:27 PM, Francesca Strappini wrote: > Dear Experts, > > I'm trying to average two monkey brains. I run this command line: > > make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkeys > > but it ended with errors. > > I run the recon-all for both monkyes with the option -notal-check > because I had problems with the Talairach registration. I don't know > if this could be the cause. > > Thanks a lot > Francesca > > Tue Mar 13 20:04:06 CET 2018 > /usr/local/freesurfer/subjects/AVGmonkeys > /usr/local/freesurfer/bin/recon-all > -s AVGmonkeys -cortribbon -aparc2aseg > subjid AVGmonkeys > setenv SUBJECTS_DIR /usr/local/freesurfer/subjects > 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 shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 > UTC 2018 x86_64 x86_64 x86_64 GNU/Linux > cputime unlimited > filesize unlimited > datasize unlimited > stacksize 8192 kbytes > coredumpsize 0 kbytes > memoryuse unlimited > vmemoryuse unlimited > descriptors 1024 > memorylocked 64 kbytes > maxproc 63682 > maxlocks unlimited > maxsignal 63682 > maxmessage 819200 > maxnice 0 > maxrtprio 0 > maxrttime unlimited > > total used free shared buff/cache > available > Mem: 16350220 4943572 7520800 278988 3885848 > 10739864 > Swap: 19528700 0 19528700 > > ######################################## > program versions used > $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ > $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ > mri_convert.bin -all-info > ProgramName: mri_convert.bin ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc > Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > FLIRT version 5.5 > $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ > mri_convert.bin --version > stable6 > ProgramName: tkregister2_cmdl ProgramArguments: --all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > Program nu_correct, built from: > Package MNI N3, version 1.12.0, compiled by nicks@terrier > (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 > ProgramName: mri_make_uchar ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc > Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mri_normalize ProgramArguments: -all-info > ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mri_watershed ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: > $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: > Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: > $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux > PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: > 40400 > ProgramName: mri_label2label.bin ProgramArguments: -all-info > ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mri_em_register ProgramArguments: -all-info > ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca > Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mri_ca_normalize ProgramArguments: -all-info > ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mri_ca_register ProgramArguments: -all-info > ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: > $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: > Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: > $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: > Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: > $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux > PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mri_tessellate ProgramArguments: -all-info > ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: > francesca Machine: shalimpc Platform: Linux PlatformVersion: > 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 > ProgramName: mri_normalize_tp2 ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: > $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: > Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: > $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: > Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mris_curvature ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: > $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: > Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mris_fix_topology ProgramArguments: -all-info > ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mris_topo_fixer ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mris_ca_label ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc > Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mris_euler_number ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mris_make_surfaces ProgramArguments: -all-info > ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mris_register ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc > Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mris_volmask ProgramArguments: --all-info > ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > CompilerName: GCC CompilerVersion: 40400 > ProgramName: mris_anatomical_stats ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: > francesca Machine: shalimpc Platform: Linux PlatformVersion: > 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 > ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: > $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: > Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mris_curvature_stats ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: > francesca Machine: shalimpc Platform: Linux PlatformVersion: > 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 > ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: > $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: > Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ > > ProgramName: mri_robust_register.bin ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: > francesca Machine: shalimpc Platform: Linux PlatformVersion: > 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 > $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ > > ProgramName: mri_robust_template ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: > 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 > ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: > $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux > PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: > $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux > PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mri_fuse_segmentations ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: > francesca Machine: shalimpc Platform: Linux PlatformVersion: > 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 > ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: > $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: > Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > CompilerVersion: 40400 > ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-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: francesca Machine: shalimpc Platform: Linux PlatformVersion: > 4.4.0-116-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 > ####################################### > #-------------------------------------------- > #@# Cortical ribbon mask Tue Mar 13 20:04:06 CET 2018 > /usr/local/freesurfer/subjects/AVGmonkeys/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 AVGmonkeys > > SUBJECTS_DIR is /usr/local/freesurfer/subjects > 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 = 34535 > writing volume /usr/local/freesurfer/subjects/AVGmonkeys/mri/ribbon.mgz > ERROR: ribbon has non-zero value at location 0,0,0 > Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 > UTC 2018 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s AVGmonkeys exited with ERRORS at Tue Mar 13 20:26:58 CET 2018 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > -- > Francesca Strappini, Ph.D. > Neurobiology Department > Weizmann Institute of Science > 234 Herzl Street, Rehovot 7610001 Israel > Tel.: +972 58 444 2584 > E-mail: francesca.strapp...@weizmann.ac.il > <mailto:francesca.strapp...@weizmann.ac.il> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
