External Email - Use Caution
Hello FreeSurfer Developers,
I'm attampting to do a structural MRI analysis with the command "recon-all -i sub102.nii.gz -s bert -all", as described in the FreeSurfer Download and Install (http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall). But I always met the error as recorded in the recon-all.log, " /home/share/test2/bert/surf mris_curvature -w lh.white.preaparc total integrated curvature = 10.012*4pi (125.809) --> -9 handles ICI = 164.9, FI = 1856.5, variation=28617.761 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux wmx 2.6.32-754.12.1.el6.x86_64 #1 SMP Tue Apr 9 14:52:26 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Mon Apr 22 11:44:12 CST 2019 " And then I checked that, the '?.white.preaparc' had been created while the '?h.white.H/K' had not, so I did some steps described in http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0, The commands "mris_curvature -w ?h.white.preaparc " and " mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated " were done to generate some files successfully. Howevere, when I continue to use "mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm <subjid> ?h curv sulc ", there were errors below: " mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm bert ?h curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/?h.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ bert/?h.smoothwm ] Reading surface...MRISread(/home/share/test2/bert/surf/?h.smoothwm): could not open file No such file or directory [ ok ] mris_curvature_stats: could not read surface file /home/share/test2/bert/surf/?h.smoothwm No such file or directory " In fact, the '?h.smoothwm' files exist and I can find it by 'ls' commond. Any help is greatly appreciated. Thanks. Mengxing Wang
can you send us the recon-all.log file? On Fri, 3 May 2019, 王梦星 wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attampting to do a structural MRI analysis with the command "recon-all -i sub102.nii.gz -s bert -all", as described in the FreeSurfer Download and Install (http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall). But I always met the error as recorded in the recon-all.log, " /home/share/test2/bert/surf mris_curvature -w lh.white.preaparc total integrated curvature = 10.012*4pi (125.809) --> -9 handles ICI = 164.9, FI = 1856.5, variation=28617.761 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux wmx 2.6.32-754.12.1.el6.x86_64 #1 SMP Tue Apr 9 14:52:26 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Mon Apr 22 11:44:12 CST 2019 " And then I checked that, the '?.white.preaparc' had been created while the '?h.white.H/K' had not, so I did some steps described in http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0, The commands "mris_curvature -w ?h.white.preaparc " and " mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated " were done to generate some files successfully. Howevere, when I continue to use "mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm <subjid> ?h curv sulc ", there were errors below: " mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm bert ?h curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/?h.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ bert/?h.smoothwm ] Reading surface...MRISread(/home/share/test2/bert/surf/?h.smoothwm): could not open file No such file or directory [ ok ] mris_curvature_stats: could not read surface file /home/share/test2/bert/surf/?h.smoothwm No such file or directory " In fact, the '?h.smoothwm' files exist and I can find it by 'ls' commond. Any help is greatly appreciated. Thanks. Mengxing Wang
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
王梦星