Re: [Freesurfer] make_average_subject monkey data

15 Mar 2018

      Thank you, Doug!
One monkey has a pretty decent registration while the other one does not
even appear in the window when I try to manually check the registration
with this command line:
tkregister --mgz --s MonkeyCelia --fstal --surf orig
It looks like if there is no brain.
2018-03-15 16:57 GMT+01:00 Douglas N. Greve dgreve@mgh.harvard.edu:
...
Check the talairach.xfm registration. It is probably way off. It does
not have to be perfect (esp since they are different species), but the
two subjects should have a similar registration
On 03/14/2018 07:27 PM, Francesca Strappini wrote:
...
Both average hemispheres look very bad, they don't even look like a
brain. The two monkey surfaces look reasonable, except for some
topological defect that I think could be fixed with some manual
editing. Is there anything I could try?
Thanks a lot
Francesca
2018-03-14 23:41 GMT+01:00 Douglas N. Greve <dgreve@mgh.harvard.edu
mailto:dgreve@mgh.harvard.edu>:
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
<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 <tel:%2B972%2058%20444%202584>
> E-mail: francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>
> <mailto:francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>>
>
>
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Re: [Freesurfer] make_average_subject monkey data