2018-03-16 16:17 GMT+01:00 Douglas Greve <dgreve@mgh.harvard.edu>:

Try this:

1. make a back up of the talairach.xfm

cp talairach.xfm bak.talarach.xfm

2. Convert the lta to an xfm:

tkregister --mov ../orig.mgz --lta talairach.lta --reg deleteme.reg.dat --xfmout talairach.xfm --s fsaverage --surfs --noedit

3. rerun make_average_subject
On 3/16/18 5:24 AM, Francesca Strappini wrote:
Thanks Doug!

Actually talairach.lta looks quite good. However, when I tried to make_average_subject with --xform talairach.lta I got immediately an error:

make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
/usr/local/freesurfer/bin/make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta

$Id: make_average_subject,v 1.23.2.1 2016/08/02 21:20:04 greve Exp $
Fri Mar 16 10:20:30 CET 2018
/usr/local/freesurfer/subjects
output ddir is /usr/local/freesurfer/subjects
uid=1000(francesca) gid=1000(francesca) groups=1000(francesca),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),113(lpadmin),128(sambashare)
make_average_surface --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
/usr/local/freesurfer/bin/make_average_surface --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta

$Id: make_average_surface,v 1.62 2016/02/16 17:17:20 zkaufman Exp $
Fri Mar 16 10:20:30 CET 2018
/usr/local/freesurfer/subjects/AVGmonkey
output ddir is /usr/local/freesurfer/subjects
uid=1000(francesca) gid=1000(francesca) groups=1000(francesca),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),113(lpadmin),128(sambashare)
====================
make_average_surface
====================
Fri Mar 16 10:20:30 CET 2018
/usr/local/freesurfer/subjects/AVGmonkey
/usr/local/freesurfer/bin/make_average_surface
--subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta
input subjects: MonkeyCelia MonkeyCassis
output subject: AVGmonkey
mri_add_xform_to_header -c auto /usr/local/freesurfer/subjects/AVGmonkey/mri/mni305.cor.mgz /usr/local/freesurfer/subjects/AVGmonkey/mri/mni305.cor.mgz
INFO: extension is mgz

#@# Making lh registration template ---------
/usr/local/freesurfer/subjects/AVGmonkey
mris_make_template -norot -annot aparc lh sphere.reg MonkeyCelia MonkeyCassis lh.reg.template.tif
not aligning hemispheres before averaging.
zeroing medial wall in aparc
creating new parameterization...

processing subject MonkeyCelia (1 of 2)
reading spherical surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/lh.sphere.reg...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/lh.inflated.H...
curvature mean = -0.074, std = 1.020
computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/lh.sulc...
computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/lh.smoothwm...

processing subject MonkeyCassis (2 of 2)
reading spherical surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.sphere.reg...
curvature mean = -0.041, std = 3.478
curvature mean = -0.056, std = 0.439
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.inflated.H...
curvature mean = -0.048, std = 1.029
computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.sulc...
computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.smoothwm...
writing updated template with 2 subjects to lh.reg.template.tif...
curvature mean = 0.038, std = 4.146
curvature mean = -0.062, std = 0.305

#@# Making rh registration template ---------
/usr/local/freesurfer/subjects/AVGmonkey
mris_make_template -norot -annot aparc rh sphere.reg MonkeyCelia MonkeyCassis rh.reg.template.tif
not aligning hemispheres before averaging.
zeroing medial wall in aparc
creating new parameterization...

processing subject MonkeyCelia (1 of 2)
reading spherical surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/rh.sphere.reg...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/rh.inflated.H...
curvature mean = -0.056, std = 0.973
computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/rh.sulc...
computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/rh.smoothwm...

processing subject MonkeyCassis (2 of 2)
reading spherical surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/rh.sphere.reg...
curvature mean = -0.081, std = 3.305
curvature mean = -0.051, std = 0.316
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/rh.inflated.H...
curvature mean = -0.059, std = 1.018
computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/rh.sulc...
computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/rh.smoothwm...
writing updated template with 2 subjects to rh.reg.template.tif...
curvature mean = 0.036, std = 4.168
curvature mean = -0.068, std = 0.371

#@# Making average lh.white surface ---------------------
Fri Mar 16 10:20:34 CET 2018
/usr/local/freesurfer/subjects/AVGmonkey
mris_make_average_surface -X talairach.lta -i 7 -o white -sdir-out /usr/local/freesurfer/subjects lh white sphere.reg AVGmonkey MonkeyCelia MonkeyCassis
using xform talairach.lta...
reading vertex positions from white...
---------------------------------------------------
hemi            = lh
avg_surf_name   = white
canon_surf_name = sphere.reg
out_sname       = AVGmonkey
xform           = talairach.lta
---------------------------------------------------

---------------------------------------------------
#@# processing subject 1/2 MonkeyCelia...
Reading /usr/local/freesurfer/subjects/MonkeyCelia/surf/lh.sphere.reg
Read /usr/local/freesurfer/subjects/MonkeyCelia/mri/T1.mgz
Surface area: 86.0 cm^2
ERROR: don't know what to do with talairach.lta
mris_average_surface failed
ERROR: make_average_surface

2018-03-15 23:18 GMT+01:00 Douglas N. Greve <dgreve@mgh.harvard.edu>:

See if the talairach.lta is any better, eg

cd subject/mri/transforms

tkregister --mov ../nu.mgz --s fsaverage --reg talairach.lta

If so, you can try running make_average_subject with --xform talairach.lta

I've never done this, but it might work :)

On 03/15/2018 01:02 PM, Francesca Strappini wrote:
> 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
> <mailto: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>
> > <mailto: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>
> > <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>
> <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>>
> > > <mailto:francesca.strappini@weizmann.ac.il
> <mailto:francesca.strappini@weizmann.ac.il>
> > <mailto:francesca.strappini@weizmann.ac.il
> <mailto:francesca.strappini@weizmann.ac.il>>>
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>

> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >

>   <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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
> <http://www.partners.org/complianceline>
> > <http://www.partners.org/complianceline
> <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.
> >
> >
> >
> >
> > --
> > 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>>
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
>
>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strappini@weizmann.ac.il
> <mailto:francesca.strappini@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

--

Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strappini@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.

Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strappini@weizmann.ac.il