That worked! Thanks a lot :) I suppose that I could improve the appearance with some further manual editing of the surfaces.
Best Francesca 2018-03-16 16:17 GMT+01:00 Douglas Greve <dgr...@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 <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 <%2B972%2058%20444%202584> >> <tel:%2B972%2058%20444%202584> <%2B972%2058%20444%202584> >> > <tel:%2B972%2058%20444%202584> <%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 <%2B972%2058%20444%202584> >> <tel:%2B972%2058%20444%202584> <%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.har >> vard.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 <%2B972%2058%20444%202584> >> > 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 <+972%2058-444-2584> > E-mail: francesca.strapp...@weizmann.ac.il > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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.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.
