Hello, I am running the command: recon-all -subjid SM2S12_autoreconall -autorecon1 -notalairach on troy and getting the following error message: --------------------------------------------- Nu Intensity Correction Thu Aug 25 12:11:42 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, -1.01845e-10, -1.20596e-09) j_ras = (-1.65567e-09, 6.42749e-09, -1) k_ras = (-2.65927e-10, 1, 9.43205e-09) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [mduff@troy:/autofs/space/troy_001/users/FREESURFER/SM2S12_autoreconall/mri/] [2005-08-25 12:11:52] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_27529/ nu0.mnc nu1.imp
/usr/pubsw/packages/mni/current/bin/volume_stats: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct recon-all exited with errors at Thu Aug 25 12:11:53 EDT 2005
This command was working yesterday, so I am not sure what has changed over night. Thanks for your help, Margaret
I'm looking into this now...
On Thu, 2005-08-25 at 12:14 -0400, Margaret Duff wrote:
Hello, I am running the command: recon-all -subjid SM2S12_autoreconall -autorecon1 -notalairach on troy and getting the following error message:
Nu Intensity Correction Thu Aug 25 12:11:42 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, -1.01845e-10, -1.20596e-09) j_ras = (-1.65567e-09, 6.42749e-09, -1) k_ras = (-2.65927e-10, 1, 9.43205e-09) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [mduff@troy:/autofs/space/troy_001/users/FREESURFER/SM2S12_autoreconall/mri/] [2005-08-25 12:11:52] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_27529/ nu0.mnc nu1.imp
/usr/pubsw/packages/mni/current/bin/volume_stats: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct recon-all exited with errors at Thu Aug 25 12:11:53 EDT 2005
This command was working yesterday, so I am not sure what has changed over night. Thanks for your help, Margaret _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Margaret,
The volume_stats tool should work for you now.
The reason for the difference is that the MNI tools were upgraded to a newer version (to v1.4, from 1.0.4), and I hadn't fully tested against all the binary/platform/machine dependencies, which can be quite complicated and exasperating!
Let me know how things work. Sorry for the delay.
Nick
On Thu, 2005-08-25 at 12:14 -0400, Margaret Duff wrote:
Hello, I am running the command: recon-all -subjid SM2S12_autoreconall -autorecon1 -notalairach on troy and getting the following error message:
Nu Intensity Correction Thu Aug 25 12:11:42 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, -1.01845e-10, -1.20596e-09) j_ras = (-1.65567e-09, 6.42749e-09, -1) k_ras = (-2.65927e-10, 1, 9.43205e-09) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [mduff@troy:/autofs/space/troy_001/users/FREESURFER/SM2S12_autoreconall/mri/] [2005-08-25 12:11:52] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_27529/ nu0.mnc nu1.imp
/usr/pubsw/packages/mni/current/bin/volume_stats: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct recon-all exited with errors at Thu Aug 25 12:11:53 EDT 2005
This command was working yesterday, so I am not sure what has changed over night. Thanks for your help, Margaret _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
hi, it seems to be working now. at least its getting further than it was before. thanks! margaret
On Thu, 25 Aug 2005, Nick Schmansky wrote:
Margaret,
The volume_stats tool should work for you now.
The reason for the difference is that the MNI tools were upgraded to a newer version (to v1.4, from 1.0.4), and I hadn't fully tested against all the binary/platform/machine dependencies, which can be quite complicated and exasperating!
Let me know how things work. Sorry for the delay.
Nick
On Thu, 2005-08-25 at 12:14 -0400, Margaret Duff wrote:
Hello, I am running the command: recon-all -subjid SM2S12_autoreconall -autorecon1 -notalairach on troy and getting the following error message:
Nu Intensity Correction Thu Aug 25 12:11:42 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, -1.01845e-10, -1.20596e-09) j_ras = (-1.65567e-09, 6.42749e-09, -1) k_ras = (-2.65927e-10, 1, 9.43205e-09) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [mduff@troy:/autofs/space/troy_001/users/FREESURFER/SM2S12_autoreconall/mri/] [2005-08-25 12:11:52] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_27529/ nu0.mnc nu1.imp
/usr/pubsw/packages/mni/current/bin/volume_stats: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct recon-all exited with errors at Thu Aug 25 12:11:53 EDT 2005
This command was working yesterday, so I am not sure what has changed over night. Thanks for your help, Margaret _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Margaret Duff -
Nick Schmansky