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 <dgr...@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 <dgr...@mgh.harvard.edu > > <mailto:dgr...@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 > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > > > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@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.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il> > > > <mailto:francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il>> > > > > <mailto:francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il> > > > <mailto:francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@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.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il> > > > <mailto:francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@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:freesur...@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.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 > -- 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
_______________________________________________ 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.
