Found a fix for that problem: http://www.mathworks.com/matlabcentral/newsreader/view_thread/284776
On Tue, 14 May 2013 14:14:31 -0400 Nick Schmansky <ni...@nmr.mgh.harvard.edu> wrote: > Joerg, > > I'm guessing you have some matlab setup script that has run prior to the > freesurfer setup. I see this output: > /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6 > > which is not something freesurfer would link against or require. > normally it should use /usr/lib64/libstdc++.so.6. > > try running this prior to sourcing the freesurfer setup: > > setenv LD_LIBRARY_PATH "" > > Glad to see 5.3 works otherwise. Thanks for testing it. > > Nick > > > > On Tue, 2013-05-14 at 15:17 +0200, Joerg Pfannmoeller wrote: > > Unfortunately encountered a problem in fs-fast stream during execution of > > selxavg3-sess. Added a relevant part of the log file below: > > > > > > >> >> >> >> >> >> >> > > sxa3pwd = > > > > /home/...removed... > > > > >> > > sxa3cmd = > > > > /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./session02 -analysis > > harm.sm0.mni305 > > > > >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m > > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > > > #@# session02 ############################### > > /home/...removed.../freesurfer_fMRT/session02 > > ------------------------- > > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ > > /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m > > /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m > > /usr/local/freesurfer/matlab/MRIread.m > > ------------------------- > > outtop = /home/...removed.../freesurfer_fMRT > > Extension format = nii.gz > > 1 stim-v-base.mat > > nruns = 1 > > autostimdur = > > > > > > outanadir = > > /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305 > > Found 45239/537168 ( 8.4) voxels in mask > > Creating Design Matrix > > ... creation time = 0.009 sec > > DoMCFit = 1 > > ntptot = 100, nX = 8, DOF = 92 > > Saving X matrix to > > /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/Xtmp.mat > > XCond = 444.207 (normalized) > > Computing compensation for resdual AR1 bias > > 1 -0.5 -0.493933 (t=0.004964) > > 2 -0.25 -0.269463 (t=0.00648) > > 3 0 -0.0514275 (t=0.00734) > > 4 0.25 0.155364 (t=0.008221) > > 5 0.5 0.337574 (t=0.009058) > > AR1 Correction M: 0.0769642 1.19552 > > Computing contrast matrices > > OLS Beta Pass > > run 1 t= 0.0 > > Global Mean 725.29 > > Global In-Mask Mean = 725.295 (694.97) > > Rescale Target = 100 > > RescaleFactor = 0.137875 > > OLS Residual Pass > > run 1 t= 0.0 > > Saving rho1 > > Smoothing ACF > > /usr/local/freesurfer/bin/mri_fwhm --mask > > /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz > > --i > > /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz > > --o > > /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz > > --fwhm 20.000000 --smooth-only > > /usr/local/freesurfer/bin/mri_fwhm: > > /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version > > `GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer/bin/mri_fwhm) > > /usr/local/freesurfer/bin/mri_fwhm: > > /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version > > `GLIBCXX_3.4.9' not found (required by /usr/local/freesurfer/bin/mri_fwhm) > > > > ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask > > /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz > > --i > > /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz > > --o > > /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz > > --fwhm 20.000000 --smooth-only > > >> ------------------------------------------ > > ERROR: fast_selxavg3() failed\n > > > > > > > > Seemingly a problem with "GLIBCXX_3.4.11". My OS is Lubuntu 13.04. > > > > > > > > > > > > > > On Tue, 14 May 2013 08:28:05 +0200 > > Joerg Pfannmoeller <pfannmo...@uni-greifswald.de> wrote: > > > > > Tested recon-all tonight on lubuntu 13.04. I did not encounter any > > > problems. Also freeview runs without an error for the subject bert. > > > > > > > > > > > > On Mon, 13 May 2013 14:40:10 +0200 > > > Jörg Pfannmöller <pfannmo...@uni-greifswald.de> wrote: > > > > > > > Just for completeness, I refer to my first contribution: > > > > > > > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Mon, 13 May 2013 13:58:30 +0200 > > > > Joerg Pfannmoeller <pfannmo...@uni-greifswald.de> wrote: > > > > > > > > > Hello Nick, > > > > > > > > > > just installed and tested the BETA version. Up to now no problem > > > > > encountered. Recon-all is just running as a test (using -use-gpu). OS > > > > > is Lubuntu 13.04. I report on the segmentation as soon as it is > > > > > finished. > > > > > > > > > > So long Joerg > > > > > > > > > > On Sun, 12 May 2013 22:41:25 -0400 (EDT) > > > > > "Nick Schmansky" <ni...@nmr.mgh.harvard.edu> wrote: > > > > > > > > > > > Fedora 18, Ubuntu 13 and Gentoo 64 users, > > > > > > > > > > > > another beta of the upcoming v5.3 is available here: > > > > > > > > > > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz > > > > > > > > > > > > this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 > > > > > > users > > > > > > who wished to test that the segfault problem in v5.2 and the prior > > > > > > beta > > > > > > v5.3 is fixed. Your help in testing this release is appreciated. > > > > > > > > > > > > Thanks, > > > > > > > > > > > > Nick > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > -- > > > > > Joerg Pfannmoeller <pfannmo...@uni-greifswald.de> > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > -- > > > > <pfannmo...@uni-greifswald.de> > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > -- > > > Joerg Pfannmoeller <pfannmo...@uni-greifswald.de> > > > > > > _______________________________________________ > > > 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 -- Joerg Pfannmoeller <pfannmo...@uni-greifswald.de> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
