The comman was mri_cvs_register --mov MAE_06072013 --mni (because labels in MNI space were mapping incorrectly to subject space -- see this thread https://www.mail-archive.com/[email protected]/msg52786.html )
The log is attached. I killed the command once I saw the errors. Thanks! Corinna On Tue, Apr 25, 2017 at 2:46 PM, Z K <[email protected]> wrote: > Hi Corinna, > > Its been awhile since Ive used Ubuntu12.04. Infact its End of Life date > is 3 days away ;) > > Can you please send me the command and the log file which gives the > exact error. Thanks. > > -Zeke > > On 04/25/2017 01:49 PM, Corinna Bauer wrote: > > Hi Zeke, > > > > I am also having this same problem. Even after completing the steps you > > listed above. I am running Ubuntu 12.04. > > > > Any suggetions? > > > > Thanks > > > > On Wed, May 28, 2014 at 1:50 PM, Z K <[email protected] > > <mailto:[email protected]>> wrote: > > > > You will need to install libboost v1.41 onto your system. You should > be > > able to install it using yum: > > > > $>yum install boost-devel > > > > However, its possible that the version you get thru this method may > be > > incompatible with the version required by freesurfer. If the above > does > > not fix your issue, then download libboost > > (http://www.boost.org/users/history/version_1_41_0.html > > <http://www.boost.org/users/history/version_1_41_0.html>) and untar > > it. Then: > > > > >cd libboost_folder > > >mkdir libraries > > >./bootstrap.sh --prefix=./libraries > > >./bjam install > > >cd libraries/lib > > > ln -s libboost_program_options.so.1.41.0 > > libboost_program_options.so.5 > > >export > > LD_LIBRARY_PATH=.../boost_temp/boost_1_41_0/libraries/ > lib:$LD_LIBRARY_PATH > > > > Hope this helps and feel free to contact me if your having issues > > getting it to work. > > > > -Zeke > > > > On 05/28/2014 12:17 PM, Michael Waskom wrote: > > > Hi, I had mri_cvs_register die on me when it couldn't find a shared > > > library. Relevant bit is (full log is attached): > > > > > > mris_resample: error while loading shared libraries: > > > libboost_program_options.so.5: cannot open shared object file: No > such > > > file or directory > > > > > > Freesurfer bugr info: > > > > > > -------------------- > > > > > > FREESURFER_HOME: /hsgs/software/freesurfer/5.3.0 > > > > > > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > > > > > RedHat release: Red Hat Enterprise Linux Server release 6.3 > (Santiago) > > > > > > Kernel info: Linux 2.6.32-358.6.2.el6.x86_64 x86_64 > > > > > > ---------------------- > > > > > > Any thoughts on how to proceed? Thanks! > > > > > > Michael > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > [email protected] <mailto:[email protected]. > harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] <mailto:[email protected]. > harvard.edu> > > 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> . 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. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
Logfile for mri_cvs_register Tue Apr 25 15:30:27 EDT 2017 --mov MAE_06072013 --mni $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ bauer Linux bauer 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux asegfname aseg Using m3z type morph files. mris_resample --atlas_reg /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/surf/lh.sphere --annot_in /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/label/lh.aparc.annot --annot_out /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/lh.resample.aparc.annot --subject_surf /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/surf/lh.white --subject_reg /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/surf/lh.cvs.tocvs_avg35_inMNI152.sphere.reg --out /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/lh.resample.white mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory mris_resample --atlas_reg /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/surf/lh.sphere --annot_in /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/label/lh.aparc.annot --annot_out /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/lh.resample.aparc.annot --subject_surf /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/surf/lh.pial --subject_reg /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/surf/lh.cvs.tocvs_avg35_inMNI152.sphere.reg --out /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/lh.resample.pial mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory mris_resample --atlas_reg /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/surf/rh.sphere --annot_in /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/label/rh.aparc.annot --annot_out /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/rh.resample.aparc.annot --subject_surf /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/surf/rh.white --subject_reg /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/surf/rh.cvs.tocvs_avg35_inMNI152.sphere.reg --out /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/rh.resample.white mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory mris_resample --atlas_reg /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/surf/rh.sphere --annot_in /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/label/rh.aparc.annot --annot_out /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/rh.resample.aparc.annot --subject_surf /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/surf/rh.pial --subject_reg /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/surf/rh.cvs.tocvs_avg35_inMNI152.sphere.reg --out /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/rh.resample.pial mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory mri_cvs_register: Step 1 (spherical registration) took 1 seconds surf2vol -fixed_mri /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/mri//norm.mgz -moving_mri /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri//norm.mgz -fixed_surf /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/surf//lh.white -moving_surf /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/lh.resample.white -fixed_surf_2 /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/surf//rh.white -moving_surf_2 /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/rh.resample.white -fixed_surf_3 /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/surf//lh.pial -moving_surf_3 /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/lh.resample.pial -fixed_surf_4 /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/surf//rh.pial -moving_surf_4 /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/rh.resample.pial -aparc /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/label//lh.aparc.annot -aparc_2 /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/label//rh.aparc.annot -aparc_3 /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/label//lh.aparc.annot -aparc_4 /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/label//rh.aparc.annot -lin_res 20 -ksp_rtol 1.0e-9 -penalty_weight 1000 -fem_steps 17 -elt_vol_range 5.0,10.0 -topology_old -compress -pc_type jacobi -ksp_type preonly -ksp_view -ksp_converged_reason -poisson .3 -young 1000 -cache_transform /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/transform.txt -out /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/el_reg_tocvs_avg35_inMNI152.mgz -out_mesh /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/el_reg_tocvs_avg35_inMNI152 -out_affine /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/el_reg_tocvs_avg35_inMNI152.affine.mgz No ASEG option present No field output option specified will use default value out_field.mgz will cache transform in file /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/cvs/transform.txt reading fixed volume reading moving volume
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