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 pfannmoelj@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 pfannmoelj@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 pfannmoelj@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" nicks@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
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